structure_analysis
Amanda Stahlke
2/28/2020
Structure
Examined “global” ancestry for all available samples. Old replicates and some suspected contamination/switching have been removed. The masterpopmap has ALL of these samples.
Admixture model, LD=0, allele freqs are uncorrelated, alpha is inferred for each popualtion.
sfiles <- list.files(path="~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/Results/",
pattern=glob2rx("outfile_*f"),full.names=TRUE)
slist <- readQ(sfiles,filetype="structure",
indlabfromfile = TRUE,
readci = TRUE)
popmap <- left_join(data.frame(sampID = rownames(slist[[1]])),
masterpopmap)## Joining, by = "sampID"## Warning: Column `sampID` joining factor and character vector, coercing into
## character vectorpopID <- data.frame(popID = popmap$popID)
popID <- data.frame(lapply(popID, as.character), stringsAsFactors=FALSE)
# sapply(popID, is.character)
pop_order <- sample_meta.dat[,c("popID", "Order")]
pop_order <- arrange(pop_order, Order)[,1]
pop_order## [1] "46CH" "1WY" "34UT" "2CO" "4CO"
## [6] "5CO" "11CO" "32UT" "31NV" "33NV"
## [11] "12AZ" "CARINA_LAB" "SUB_LAB" "44GR" "43GR"
## [16] "39CR" "38CR" "37CR" "40CR" "41CR"
## [21] "42CR" "6KS" "8OK" "28NM" "26NM"
## [26] "27NM" "15TX" "19TX" "21NM" "16TX"
## [31] "20NM" "18TX" "52TX" "50TX" "51TX"
## [36] "47TX" "49TX"samplesize <- left_join(popmap, sample_meta.dat) %>%
count(popID) %>%
merge(sample_meta.dat)## Joining, by = "popID"write.table(samplesize, "pop_metadata_samplesize.tsv", sep = "\t", row.names = F, quote = F)What is the best K?
sr1 <- summariseQ(tabulateQ(slist))
p <- evannoMethodStructure(data=sr1,exportplot=F,returnplot=T,returndata=F,basesize=12,linesize=0.7)
grid.arrange(p)
evannoMethodStructure(data=sr1,
exportplot=T,
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "global_deltaK",
returndata=F,
height = 10, width = 9)K=2 and K=3 are super stable. D. carinata appears as a mix between sublineata and elongata. I am surprised to see, for the first time in these samples, indications of admixture between carinlata and sublineata along the Rio Grande.
k2 <- plotQ(alignK(slist[c(21:30)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
subsetgrp = pop_order,
ordergrp = T,
grplab = popID,
linepos = 1,
grplabangle=-45,
grplabpos = 0,
grplabheight=20)
grid.arrange(k2$plot[[1]])
k3 <- plotQ(alignK(slist[c(31:40)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
ordergrp = T,
grplab = popID,
grplabangle=-90)
grid.arrange(k3$plot[[1]])
As usual, K=4 reflects lab populations, elongata in the native range, and hints at carinulata substructure.
k4 <- plotQ(alignK(slist[c(41:50)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
grplab = popID,
ordergrp = T,
grplabangle=-90)
grid.arrange(k4$plot[[1]])
k5 <- plotQ(alignK(slist[c(51:60)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
grplab = popID,
ordergrp = T,
grplabangle=-90)
grid.arrange(k5$plot[[1]])
k6 <- plotQ(alignK(slist[c(61:70)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
grplab = popID,
ordergrp = T,
grplabangle=-90)
grid.arrange(k6$plot[[1]])
k7 <- plotQ(alignK(slist[c(71:80)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
grplab = popID,
grplabangle=-90)
grid.arrange(k7$plot[[1]])
k8 <- plotQ(alignK(slist[c(81:90)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
# clustercol=cbbPalette,
grplab = popID,
grplabangle=-90)
grid.arrange(k8$plot[[1]])
plotQMultiline(slist[41],
showticks=T,
clustercol=cbbPalette,
grplab = popID,
ordergrp=TRUE,
spl = 25,
showindlab = T,
showyaxis = T,
barsize = .9,
subsetgrp = pop_order,
basesize=11,
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "multilineK4",
useindlab = T)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/multilineK4-1.png exported.
## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/multilineK4-2.png exported.
## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/multilineK4-3.png exported.plotQ(alignK(slist[c(21:30)]),
imgoutput="join",
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "Joined-K2",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=cbbPalette,
subsetgrp = pop_order,
height = .1,
ordergrp = T,
grplab = popID,
linepos = 1,
divtype = 1,
grplabangle=45,
grplabpos = .8,
grplabspacer = 0,
grplabheight=70,
width=100,
showtitle=T,
grplabsize = 4,
titlelab="Global Population Structure, K=2",
titlesize = 20)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/Joined-K2.png exported.plotQ(alignK(slist[c(31:40)]),
imgoutput="join",
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "Joined-K3",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=cbbPalette,
subsetgrp = pop_order,
height = .1,
ordergrp = T,
grplab = popID,
linepos = 1,
divtype = 1,
grplabangle=45,
grplabpos = .8,
grplabspacer = 0,
grplabheight=70,
width=100,
showtitle=T,
grplabsize = 4,
titlelab="Global Population Structure, K=3",
titlesize = 20)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/Joined-K3.png exported.plotQ(alignK(slist[c(41:50)]),
imgoutput="join",
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "Joined-K4",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=cbbPalette,
subsetgrp = pop_order,
height = .1,
ordergrp = T,
grplab = popID,
linepos = 1,
divtype = 1,
grplabangle=45,
grplabpos = .8,
grplabspacer = 0,
grplabheight=70,
width=100,
showtitle=T,
grplabsize = 4,
titlelab="Global Population Structure, K=4",
titlesize = 20)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/Joined-K4.png exported.plotQ(alignK(slist[c(51:60)]),
imgoutput="join",
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "Joined-K5",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=cbbPalette,
subsetgrp = pop_order,
height = .1,
ordergrp = T,
grplab = popID,
linepos = 1,
divtype = 1,
grplabangle=45,
grplabpos = .8,
grplabspacer = 0,
grplabheight=70,
width=100,
showtitle=T,
grplabsize = 4,
titlelab="Global Population Structure, K=5",
titlesize = 20)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/Joined-K5.png exported.plotQ(alignK(slist[c(61:70)]),
imgoutput="join",
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "Joined-K6",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=cbbPalette,
subsetgrp = pop_order,
height = .1,
ordergrp = T,
grplab = popID,
linepos = 1,
divtype = 1,
grplabangle=45,
grplabpos = .8,
grplabspacer = 0,
grplabheight=70,
width=100,
showtitle=T,
grplabsize = 4,
titlelab="Global Population Structure, K=6",
titlesize = 20)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/Joined-K6.png exported.plotQ(alignK(slist[c(71:80)]),
imgoutput="join",
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "Joined-K7",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=cbbPalette,
subsetgrp = pop_order,
height = .1,
ordergrp = T,
grplab = popID,
linepos = 1,
divtype = 1,
grplabangle=45,
grplabpos = .8,
grplabspacer = 0,
grplabheight=70,
width=100,
showtitle=T,
grplabsize = 4,
titlelab="Global Population Structure, K=7",
titlesize = 20)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/Joined-K7.png exported.## extract one q file that reflects known species identity
global_k4_q <- slist[[41]]
global_k4_q$sampID <- row.names(global_k4_q)
## which cluster is carinulata?
gr_samples <- masterpopmap[grep( "CR", masterpopmap[,2]), ]
gr_q <- semi_join(global_k4_q, gr_samples)
max_cl_gr <- sapply(gr_q[,1:4], max)
elongata_cluster <- which(colnames(gr_q) == colnames(gr_q[which(max_cl_gr==1)]))
elongata_cluster## [1] 1## which cluster is elongata?
ch_samples <- masterpopmap[grep( "CH", masterpopmap[,2]), ]
ch_q <- semi_join(global_k4_q, ch_samples)
max_cl_ch <- sapply(ch_q[,1:4], max)
carinulata_cluster <- which(colnames(ch_q) == colnames(ch_q[which(max_cl_ch==1)]))
carinulata_cluster## [1] 3## which cluster is sublineata?
sub_samples <- masterpopmap[grep( "SUB_LAB", masterpopmap[,2]), ]
sub_q <- semi_join(global_k4_q, sub_samples)
max_cl_sub <- sapply(sub_q[,1:4], max)
sublineata_cluster <- which(colnames(sub_q) == colnames(sub_q[which(max_cl_sub==1)]))
## which cluster is carinata?
carina_samples <- masterpopmap[grep( "CARINA_LAB", masterpopmap[,2]),]
carina_q <- semi_join(global_k4_q, carina_samples)
max_cl_cara <- sapply(carina_q[,1:4], max)
carinata_cluster <- which(colnames(carina_q) == colnames(carina_q[which(max_cl_cara==1)]))
cls <- c(carinata_cluster, carinulata_cluster, sublineata_cluster, elongata_cluster)
spp <- c("carinata", "carinulata", "sublineata", "elongata")
clusters <- as.data.frame(cbind(spp = spp[order(cls)], cluster = seq(1,4)))
colnames(global_k4_q)[1:4] <- as.character(clusters$spp)
q_popmap <- merge(global_k4_q, popmap)
head(q_popmap)## sampID elongata carinata carinulata sublineata popID
## 1 D1 1.000 0 0.000 0.000 38CR
## 2 D12 1.000 0 0.000 0.000 41CR
## 3 D13 1.000 0 0.000 0.000 41CR
## 4 D15_rep 0.936 0 0.058 0.006 41CR
## 5 D16 1.000 0 0.000 0.000 41CR
## 6 D17 1.000 0 0.000 0.000 43GR## slist[43]
## 1 = elongata
## 2 = carinata
## 3 = sub
## 4 = carinu
legend <- merge(legend_colors, clusters)
clustercols <- arrange(legend, cluster) %>%
select(cbbPalette)
clustercols <- clustercols$cbbPalette
legendlab <- arrange(legend, cluster) %>%
mutate(label = paste("D. ", spp))
legendlab <- legendlab$label[1:4]
plotQ(slist[41],
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "MainTextFigure_K4",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=clustercols,
subsetgrp = pop_order,
ordergrp = T,
grplab = popID,
linepos = 1,
linesize=0.8,
pointsize = 5,
divtype = 1,
grplabangle= 90,
grplabpos = .9,
grplabspacer = 0,
grplabheight=35,
grplabsize = 10,
height = .05,
width=100,
showlegend = T, legendkeysize=30,legendtextsize=30, legendpos="left", legendlab=legendlab,
# titlelab="Global Population Structure K=4",
# titlesize = 20,
basesize=30)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/MainTextFigure_K4.png exported.# custom strip panel label showing k only
fn1 <- function(x) attr(x,"k")
spnames <- paste0("K=",sapply(slist,fn1))
# Combine K=2, K=3, K=4
k2k3k4 <- c(21,31,41)
plotQ(slist[k2k3k4],
imgoutput="join",
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "Joined-K2-K3-K4",
exportplot=T,
showyaxis=T,
splab=spnames[k2k3k4],
splabsize= 20,
clustercol=clustercols,
subsetgrp = pop_order,
height = .1,
ordergrp = T,
grplab = popID,
linepos = 1,
divtype = 1,
grplabangle= 90,
grplabpos = .8,
grplabspacer = 0,
grplabheight=70,
width=100,
showtitle=T,
grplabsize = 8,
# showlegend = T,
# legendkeysize=20,legendtextsize=20, legendpos="right", legendlab=legendlab,
titlelab="Global Population Structure across K",
titlesize = 20)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/Joined-K2-K3-K4.png exported.## Plot subsets of the whole set
subset1 <- sample_meta.dat %>%
arrange(Order) %>%
select(popID) %>%
slice(1:20)
subset2 <- sample_meta.dat %>%
arrange(Order) %>%
select(popID) %>%
slice(21:nrow(sample_meta.dat))
plotQ(slist[41],
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "subset1_global",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=clustercols,
subsetgrp=as.character(subset1$popID),
ordergrp = T,
grplab = popID,
linepos = .98,
linesize=0.8,
pointsize = 5,
divtype = 1,
grplabangle= 90,
grplabpos = .9,
grplabspacer = 0,
grplabheight=55,
grplabsize = 20,
height = .05,
width=100,
showlegend = T, legendkeysize=30,legendtextsize=30, legendpos="left", legendlab=legendlab,
basesize=30)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/subset1_global.png exported.plotQ(slist[41],
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/",
outputfilename = "subset2_global",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=clustercols,
subsetgrp=as.character(subset2$popID),
ordergrp = T,
grplab = popID,
linepos = 1,
linesize=0.8,
pointsize = 5,
divtype = 1,
grplabangle= 90,
grplabpos = .9,
grplabspacer = 0,
grplabheight=45,
grplabsize = 20,
height = .05,
width=100,
basesize=30)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/structure_analysis/plots/subset2_global.png exported.## subset individuals for substructure of elongata
elongata <- filter(global_k4_q, elongata > .1) %>%
select('sampID')
nrow(elongata)## [1] 98elongata_popmap <- semi_join(popmap, elongata)## Joining, by = "sampID"write.table(elongata_popmap,
file = "../info/elongata_popmap.tsv",
sep = "\t",
quote=F, col.names = F, row.names = F)
## subset individuals for substructure of elongata
carinulata <- filter(global_k4_q, carinulata > .1) %>%
select('sampID')
nrow(carinulata)## [1] 182carinulata_popmap <- semi_join(popmap, carinulata)## Joining, by = "sampID"write.table(carinulata_popmap,
file = "../info/carinulata_popmap.tsv",
sep = "\t",
quote=F, col.names = F, row.names = F)
## Are population genetic statistics (like private alleles etc) to populations filtering?
others_popmap <- anti_join(popmap, carinulata)## Joining, by = "sampID"write.table(others_popmap,
file = "../info/others_popmap.tsv",
sep = "\t",
quote=F, col.names = F, row.names = F)Which sites have individuals with admxiture?
sample_size <- samplesize %>%
select('popID', 'n')
num_admixed_inds <- q_popmap %>%
filter_at(vars(elongata:sublineata),
~ . < .95) %>%
group_by(popID) %>%
count(popID)
colnames(num_admixed_inds)[2] <- 'num_admixed'
num_admixed_inds## # A tibble: 14 x 2
## # Groups: popID [14]
## popID num_admixed
## <chr> <int>
## 1 15TX 4
## 2 16TX 1
## 3 18TX 2
## 4 19TX 4
## 5 20NM 5
## 6 21NM 4
## 7 26NM 13
## 8 27NM 4
## 9 28NM 8
## 10 37CR 1
## 11 41CR 1
## 12 44GR 1
## 13 47TX 1
## 14 6KS 1merge(sample_size, num_admixed_inds) %>%
mutate(perc_admixed = num_admixed/n) %>%
arrange(desc(perc_admixed))## popID n num_admixed perc_admixed
## 1 26NM 18 13 0.72222222
## 2 28NM 17 8 0.47058824
## 3 20NM 17 5 0.29411765
## 4 21NM 14 4 0.28571429
## 5 19TX 15 4 0.26666667
## 6 15TX 16 4 0.25000000
## 7 27NM 20 4 0.20000000
## 8 37CR 6 1 0.16666667
## 9 18TX 17 2 0.11764706
## 10 6KS 10 1 0.10000000
## 11 41CR 16 1 0.06250000
## 12 44GR 16 1 0.06250000
## 13 16TX 18 1 0.05555556
## 14 47TX 25 1 0.04000000q_popmap %>%
filter_at(vars(elongata:sublineata),
~ . < .95) %>%
group_by(popID) %>%
summarize_at(vars(carinata:sublineata), funs(mean, var))## Warning: funs() is soft deprecated as of dplyr 0.8.0
## Please use a list of either functions or lambdas:
##
## # Simple named list:
## list(mean = mean, median = median)
##
## # Auto named with `tibble::lst()`:
## tibble::lst(mean, median)
##
## # Using lambdas
## list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
## This warning is displayed once per session.## # A tibble: 14 x 7
## popID carinata_mean carinulata_mean sublineata_mean carinata_var
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 15TX 0.821 0 0.0452 0.00391
## 2 16TX 0.875 0 0.125 NA
## 3 18TX 0.332 0.0455 0.622 0.218
## 4 19TX 0.901 0.0248 0.0742 0.00178
## 5 20NM 0.225 0 0.757 0.0559
## 6 21NM 0.0792 0.00025 0.854 0.0150
## 7 26NM 0.171 0.000308 0.809 0.0171
## 8 27NM 0.143 0 0.846 0.0214
## 9 28NM 0.382 0.201 0.415 0.0546
## 10 37CR 0 0.114 0 NA
## 11 41CR 0 0.058 0.006 NA
## 12 44GR 0 0.058 0 NA
## 13 47TX 0 0.094 0.905 NA
## 14 6KS 0 0.091 0.909 NA
## # … with 2 more variables: carinulata_var <dbl>, sublineata_var <dbl>Which sites have multiple spp, even without admixture?
foo <- q_popmap %>%
filter_all(any_vars(. > .95)) %>%
group_by(popID) %>%
summarize_at(vars(elongata:sublineata), funs(sum)) %>%
merge(sample_size)
max_ancestry <- apply(X=foo[,2:5], MARGIN=1, FUN=max)
### if a cluster has less than foo$sample_size-.5, will return any pop with an ind less than 50% of majority ancestry
mixed_pops <- foo[foo$n - .5 > max_ancestry,]
mixed_pops## popID elongata carinata carinulata sublineata n
## 3 15TX 1.538 14.265 0.004 0.187 16
## 4 16TX 16.992 0.875 0.001 0.131 18
## 5 18TX 0.000 0.664 2.143 14.191 17
## 6 19TX 0.001 14.484 0.130 0.384 15
## 8 20NM 0.090 1.138 0.004 15.768 17
## 9 21NM 0.273 0.337 0.008 13.381 14
## 10 26NM 0.285 2.221 0.004 15.486 18
## 11 27NM 0.222 0.604 0.001 19.172 20
## 12 28NM 0.019 5.045 8.597 3.339 17
## 32 6KS 0.000 7.964 1.091 0.945 10perc_admixed <- merge(sample_size, num_admixed_inds) %>%
mutate(perc_admixed = num_admixed/n) %>%
arrange(desc(perc_admixed))
perc_admixed## popID n num_admixed perc_admixed
## 1 26NM 18 13 0.72222222
## 2 28NM 17 8 0.47058824
## 3 20NM 17 5 0.29411765
## 4 21NM 14 4 0.28571429
## 5 19TX 15 4 0.26666667
## 6 15TX 16 4 0.25000000
## 7 27NM 20 4 0.20000000
## 8 37CR 6 1 0.16666667
## 9 18TX 17 2 0.11764706
## 10 6KS 10 1 0.10000000
## 11 41CR 16 1 0.06250000
## 12 44GR 16 1 0.06250000
## 13 16TX 18 1 0.05555556
## 14 47TX 25 1 0.04000000mix_admix <- full_join(mixed_pops, perc_admixed[,c('popID', 'perc_admixed')]) %>%
arrange(desc(perc_admixed)) ## Joining, by = "popID"mix_admix## popID elongata carinata carinulata sublineata n perc_admixed
## 1 26NM 0.285 2.221 0.004 15.486 18 0.72222222
## 2 28NM 0.019 5.045 8.597 3.339 17 0.47058824
## 3 20NM 0.090 1.138 0.004 15.768 17 0.29411765
## 4 21NM 0.273 0.337 0.008 13.381 14 0.28571429
## 5 19TX 0.001 14.484 0.130 0.384 15 0.26666667
## 6 15TX 1.538 14.265 0.004 0.187 16 0.25000000
## 7 27NM 0.222 0.604 0.001 19.172 20 0.20000000
## 8 37CR NA NA NA NA NA 0.16666667
## 9 18TX 0.000 0.664 2.143 14.191 17 0.11764706
## 10 6KS 0.000 7.964 1.091 0.945 10 0.10000000
## 11 41CR NA NA NA NA NA 0.06250000
## 12 44GR NA NA NA NA NA 0.06250000
## 13 16TX 16.992 0.875 0.001 0.131 18 0.05555556
## 14 47TX NA NA NA NA NA 0.04000000There may be almost no population that is completely pure. How many ‘pure’ sites did we detect?
setdiff(popmap$popID, mix_admix$popID )## [1] "11CO" "12AZ" "1WY" "2CO" "31NV"
## [6] "32UT" "33NV" "34UT" "38CR" "39CR"
## [11] "43GR" "46CH" "49TX" "4CO" "50TX"
## [16] "51TX" "52TX" "5CO" "8OK" "CARINA_LAB"
## [21] "SUB_LAB"Among individuals, how many pure? How many hybrids, and of what type?
ci <- data.frame(attributes(slist[[41]])$ci)
colnames(ci) <- paste0(rep(colnames(global_k4_q)[1:4], each=2),
"_", rep(c("L", "H"), times = 4))
ci <- cbind(ci, global_k4_q)
ci <- merge(ci, masterpopmap)
ci## sampID elongata_L elongata_H carinata_L carinata_H carinulata_L
## 1 D1 0.999 1.000 0.000 0.001 0.000
## 2 D12 0.998 1.000 0.000 0.001 0.000
## 3 D13 0.999 1.000 0.000 0.001 0.000
## 4 D15_rep 0.914 0.956 0.000 0.001 0.039
## 5 D16 0.999 1.000 0.000 0.001 0.000
## 6 D17 0.998 1.000 0.000 0.001 0.000
## 7 D18 0.998 1.000 0.000 0.001 0.000
## 8 D19 0.998 1.000 0.000 0.001 0.000
## 9 D2 0.999 1.000 0.000 0.001 0.000
## 10 D20 0.998 1.000 0.000 0.001 0.000
## 11 D21 0.997 1.000 0.000 0.001 0.000
## 12 D22 0.998 1.000 0.000 0.001 0.000
## 13 D23 0.998 1.000 0.000 0.001 0.000
## 14 D24_rep 0.921 0.962 0.000 0.001 0.038
## 15 D27 0.998 1.000 0.000 0.001 0.000
## 16 D3 0.998 1.000 0.000 0.001 0.000
## 17 D33 0.998 1.000 0.000 0.001 0.000
## 18 D34 0.999 1.000 0.000 0.001 0.000
## 19 D35 0.997 1.000 0.000 0.001 0.000
## 20 D37 0.999 1.000 0.000 0.001 0.000
## 21 D38 0.998 1.000 0.000 0.001 0.000
## 22 D39 0.998 1.000 0.000 0.001 0.000
## 23 D4 0.999 1.000 0.000 0.001 0.000
## 24 D40 0.998 1.000 0.000 0.001 0.000
## 25 D41 0.998 1.000 0.000 0.001 0.000
## 26 D42 0.998 1.000 0.000 0.001 0.000
## 27 D43 0.998 1.000 0.000 0.001 0.000
## 28 D44 0.998 1.000 0.000 0.001 0.000
## 29 D46 0.999 1.000 0.000 0.001 0.000
## 30 D47 0.999 1.000 0.000 0.001 0.000
## 31 D48 0.999 1.000 0.000 0.001 0.000
## 32 D49 0.998 1.000 0.000 0.001 0.000
## 33 D5 0.999 1.000 0.000 0.001 0.000
## 34 D50 0.998 1.000 0.000 0.001 0.000
## 35 D51 0.998 1.000 0.000 0.001 0.000
## 36 D52 0.999 1.000 0.000 0.001 0.000
## 37 D53 0.998 1.000 0.000 0.001 0.000
## 38 D54 0.998 1.000 0.000 0.001 0.000
## 39 D55 0.999 1.000 0.000 0.001 0.000
## 40 D56 0.999 1.000 0.000 0.001 0.000
## 41 D57 0.999 1.000 0.000 0.001 0.000
## 42 D58 0.998 1.000 0.000 0.001 0.000
## 43 D59 0.999 1.000 0.000 0.001 0.000
## 44 D6 0.999 1.000 0.000 0.001 0.000
## 45 D60 0.998 1.000 0.000 0.001 0.000
## 46 D61 0.999 1.000 0.000 0.001 0.000
## 47 D62 0.998 1.000 0.000 0.001 0.000
## 48 D63 0.997 1.000 0.000 0.001 0.000
## 49 D64 0.998 1.000 0.000 0.001 0.000
## 50 D65_rep 0.985 1.000 0.000 0.001 0.000
## 51 D7 0.999 1.000 0.000 0.001 0.000
## 52 D70_rep 0.860 0.909 0.000 0.001 0.090
## 53 D71_rep 0.991 1.000 0.000 0.001 0.000
## 54 D72 0.997 1.000 0.000 0.001 0.000
## 55 D73 0.998 1.000 0.000 0.001 0.000
## 56 D75 0.998 1.000 0.000 0.001 0.000
## 57 D76 0.998 1.000 0.000 0.001 0.000
## 58 D77 0.998 1.000 0.000 0.001 0.000
## 59 D78 0.999 1.000 0.000 0.001 0.000
## 60 D79 0.999 1.000 0.000 0.001 0.000
## 61 D8 0.999 1.000 0.000 0.001 0.000
## 62 D80 0.999 1.000 0.000 0.001 0.000
## 63 D81 0.999 1.000 0.000 0.001 0.000
## 64 D82 0.998 1.000 0.000 0.001 0.000
## 65 D83 0.999 1.000 0.000 0.001 0.000
## 66 D84 0.998 1.000 0.000 0.001 0.000
## 67 D85 0.998 1.000 0.000 0.001 0.000
## 68 D86 0.998 1.000 0.000 0.001 0.000
## 69 D87 0.997 1.000 0.000 0.001 0.000
## 70 D88 0.998 1.000 0.000 0.001 0.000
## 71 D89 0.997 1.000 0.000 0.001 0.000
## 72 D90 0.997 1.000 0.000 0.001 0.000
## 73 D91 0.998 1.000 0.000 0.001 0.000
## 74 D92 0.997 1.000 0.000 0.001 0.000
## 75 D93 0.997 1.000 0.000 0.001 0.000
## 76 D94 0.997 1.000 0.000 0.001 0.000
## 77 E1 0.000 0.001 0.000 0.001 0.999
## 78 E10 0.000 0.001 0.000 0.001 0.999
## 79 E11 0.000 0.001 0.000 0.001 0.999
## 80 E12 0.000 0.001 0.000 0.001 0.999
## 81 E13 0.000 0.001 0.000 0.001 0.999
## 82 E15_rep 0.000 0.001 0.000 0.001 0.999
## 83 E17 0.000 0.001 0.000 0.001 0.999
## 84 E18 0.000 0.001 0.000 0.001 0.999
## 85 E19 0.000 0.001 0.000 0.001 0.999
## 86 E20 0.000 0.001 0.000 0.001 0.999
## 87 E21 0.000 0.001 0.000 0.001 0.999
## 88 E22 0.000 0.001 0.000 0.001 0.999
## 89 E23 0.000 0.001 0.000 0.001 0.999
## 90 E24_rep 0.000 0.001 0.000 0.001 0.998
## 91 E25 0.000 0.001 0.000 0.001 0.999
## 92 E26 0.000 0.001 0.000 0.001 0.999
## 93 E27 0.000 0.001 0.000 0.001 0.999
## 94 E28 0.000 0.001 0.000 0.001 0.999
## 95 E29 0.205 0.291 0.709 0.794 0.000
## 96 E3 0.000 0.001 0.000 0.001 0.999
## 97 E30 0.000 0.001 0.990 1.000 0.000
## 98 E31 0.000 0.001 0.000 0.001 0.999
## 99 E32 0.000 0.001 0.000 0.001 0.999
## 100 E33 0.000 0.001 0.000 0.001 0.999
## 101 E34 0.000 0.001 0.000 0.001 0.999
## 102 E35 0.000 0.001 0.000 0.001 0.999
## 103 E36 0.000 0.001 0.000 0.001 0.999
## 104 E37 0.000 0.001 0.000 0.001 0.999
## 105 E38 0.000 0.001 0.000 0.001 0.999
## 106 E39 0.000 0.001 0.000 0.001 0.999
## 107 E4 0.000 0.001 0.000 0.001 0.999
## 108 E40 0.000 0.001 0.000 0.001 0.999
## 109 E41 0.000 0.001 0.000 0.001 0.999
## 110 E42 0.000 0.001 0.000 0.001 0.999
## 111 E43 0.000 0.001 0.000 0.001 0.999
## 112 E44 0.000 0.001 0.000 0.001 0.999
## 113 E45 0.000 0.001 0.000 0.001 0.999
## 114 E46 0.000 0.001 0.000 0.001 0.999
## 115 E47 0.000 0.001 0.000 0.001 0.999
## 116 E48 0.000 0.001 0.000 0.001 0.999
## 117 E49 0.000 0.001 0.000 0.001 0.999
## 118 E5 0.000 0.001 0.000 0.001 0.999
## 119 E50 0.000 0.001 0.000 0.001 0.999
## 120 E51 0.000 0.001 0.000 0.001 0.999
## 121 E52 0.000 0.001 0.000 0.001 0.999
## 122 E53 0.000 0.001 0.000 0.001 0.999
## 123 E54 0.000 0.001 0.000 0.001 0.999
## 124 E55 0.000 0.001 0.000 0.001 0.999
## 125 E56 0.000 0.001 0.000 0.001 0.999
## 126 E57 0.000 0.001 0.000 0.001 0.999
## 127 E58 0.000 0.001 0.000 0.001 0.999
## 128 E59 0.000 0.001 0.000 0.001 0.999
## 129 E60 0.000 0.001 0.000 0.001 0.999
## 130 E61 0.000 0.001 0.000 0.001 0.999
## 131 E62 0.000 0.001 0.000 0.001 0.999
## 132 E63 0.000 0.001 0.000 0.001 0.999
## 133 E64 0.000 0.001 0.000 0.001 0.999
## 134 E65 0.000 0.001 0.000 0.001 0.998
## 135 E67 0.000 0.001 0.000 0.001 0.999
## 136 E68 0.000 0.001 0.000 0.001 0.999
## 137 E69 0.000 0.001 0.000 0.001 0.999
## 138 E7 0.000 0.001 0.000 0.001 0.999
## 139 E70 0.000 0.001 0.000 0.001 0.998
## 140 E75 0.000 0.001 0.000 0.001 0.999
## 141 E76 0.000 0.001 0.000 0.001 0.999
## 142 E77 0.000 0.001 0.000 0.001 0.999
## 143 E78 0.000 0.001 0.000 0.001 0.999
## 144 E8 0.000 0.001 0.000 0.001 0.999
## 145 E82 0.000 0.001 0.000 0.001 0.999
## 146 E84 0.000 0.001 0.000 0.001 0.999
## 147 E85 0.000 0.001 0.000 0.001 0.999
## 148 E86 0.000 0.001 0.000 0.001 0.999
## 149 E87 0.000 0.001 0.000 0.001 0.999
## 150 E9 0.000 0.001 0.000 0.001 0.999
## 151 E90 0.000 0.001 0.000 0.001 0.999
## 152 E92 0.000 0.001 0.000 0.001 0.999
## 153 E94 0.000 0.001 0.000 0.001 0.999
## 154 E95 0.000 0.001 0.000 0.001 0.998
## 155 F1 0.000 0.001 0.000 0.001 0.999
## 156 F10 0.000 0.001 0.000 0.001 0.999
## 157 F11 0.000 0.001 0.000 0.001 0.998
## 158 F12 0.000 0.001 0.000 0.001 0.999
## 159 F13 0.000 0.001 0.000 0.001 0.999
## 160 F14 0.000 0.001 0.000 0.001 0.999
## 161 F15 0.000 0.001 0.000 0.001 0.999
## 162 F16 0.000 0.001 0.000 0.001 0.999
## 163 F17 0.000 0.001 0.000 0.001 0.999
## 164 F18 0.000 0.001 0.000 0.001 0.999
## 165 F19 0.000 0.001 0.000 0.006 0.991
## 166 F2 0.000 0.001 0.000 0.001 0.999
## 167 F20 0.000 0.001 0.000 0.001 0.999
## 168 F21 0.000 0.001 0.000 0.001 0.995
## 169 F22 0.000 0.001 0.000 0.001 0.999
## 170 F23 0.000 0.001 0.000 0.001 0.999
## 171 F24 0.000 0.001 0.000 0.001 0.999
## 172 F25 0.000 0.001 0.000 0.001 0.999
## 173 F26 0.000 0.001 0.000 0.001 0.999
## 174 F27 0.000 0.001 0.000 0.001 0.999
## 175 F28 0.000 0.001 0.000 0.001 0.999
## 176 F29 0.000 0.001 0.997 1.000 0.000
## 177 F30 0.000 0.001 0.997 1.000 0.000
## 178 F33 0.000 0.001 0.943 1.000 0.000
## 179 F34 0.000 0.001 0.997 1.000 0.000
## 180 F35 0.000 0.001 0.998 1.000 0.000
## 181 F36 0.000 0.001 0.997 1.000 0.000
## 182 F37 0.000 0.001 0.000 0.001 0.999
## 183 F38 0.000 0.001 0.000 0.001 0.999
## 184 F39 0.000 0.001 0.000 0.001 0.999
## 185 F4 0.000 0.001 0.000 0.001 0.999
## 186 F41 0.000 0.001 0.920 1.000 0.000
## 187 F42 0.000 0.001 0.995 1.000 0.000
## 188 F43 0.000 0.001 0.998 1.000 0.000
## 189 F44 0.000 0.001 0.998 1.000 0.000
## 190 F45 0.000 0.001 0.996 1.000 0.000
## 191 F46 0.000 0.001 0.988 1.000 0.000
## 192 F47 0.000 0.001 0.996 1.000 0.000
## 193 F48 0.000 0.001 0.995 1.000 0.000
## 194 F49 0.000 0.001 0.000 0.001 0.999
## 195 F5 0.000 0.001 0.000 0.001 0.999
## 196 F50 0.000 0.001 0.000 0.001 0.999
## 197 F51 0.000 0.001 0.000 0.001 0.991
## 198 F52 0.000 0.001 0.000 0.001 0.999
## 199 F54 0.999 1.000 0.000 0.001 0.000
## 200 F55 0.000 0.001 0.998 1.000 0.000
## 201 F56 0.000 0.001 0.997 1.000 0.000
## 202 F57 0.000 0.001 0.998 1.000 0.000
## 203 F58 0.000 0.001 0.998 1.000 0.000
## 204 F59 0.000 0.001 0.000 0.001 0.999
## 205 F60 0.000 0.001 0.000 0.001 0.999
## 206 F61 0.000 0.001 0.000 0.001 0.999
## 207 F62 0.000 0.001 0.000 0.001 0.999
## 208 F63 0.000 0.001 0.998 1.000 0.000
## 209 F64 0.000 0.001 0.967 1.000 0.000
## 210 F65 0.999 1.000 0.000 0.001 0.000
## 211 F66 0.998 1.000 0.000 0.001 0.000
## 212 F67 0.000 0.001 0.997 1.000 0.000
## 213 F68 0.000 0.022 0.976 1.000 0.000
## 214 F69 0.000 0.001 0.998 1.000 0.000
## 215 F70 0.000 0.001 0.997 1.000 0.000
## 216 F71 0.000 0.001 0.000 0.001 0.998
## 217 F72 0.000 0.001 0.000 0.001 0.999
## 218 F73 0.000 0.001 0.000 0.001 0.999
## 219 F74 0.000 0.001 0.000 0.001 0.998
## 220 F75 0.000 0.001 0.000 0.001 0.000
## 221 F76 0.000 0.001 0.000 0.001 0.000
## 222 F77 0.000 0.001 0.000 0.001 0.000
## 223 F78 0.005 0.044 0.036 0.110 0.000
## 224 F79 0.000 0.001 0.991 1.000 0.000
## 225 F80 0.000 0.001 0.991 1.000 0.000
## 226 F81 0.000 0.001 0.998 1.000 0.000
## 227 F82 0.000 0.001 0.996 1.000 0.000
## 228 F83 0.000 0.001 0.000 0.002 0.000
## 229 F84 0.022 0.055 0.050 0.128 0.000
## 230 F85 0.998 1.000 0.000 0.001 0.000
## 231 F86 0.000 0.001 0.996 1.000 0.000
## 232 F87 0.000 0.026 0.959 1.000 0.000
## 233 F88 0.000 0.001 0.997 1.000 0.000
## 234 F89 0.000 0.001 0.946 1.000 0.000
## 235 F9 0.000 0.001 0.000 0.001 0.998
## 236 F90 0.000 0.001 0.996 1.000 0.000
## 237 F91_2019 0.000 0.001 0.000 0.001 0.999
## 238 F92 0.000 0.001 0.419 0.541 0.000
## 239 F93 0.000 0.001 0.000 0.004 0.000
## 240 F94 0.000 0.054 0.099 0.202 0.000
## 241 F95 0.000 0.001 0.054 0.126 0.000
## 242 F96 0.000 0.015 0.269 0.384 0.000
## 243 G01_rep 0.106 0.161 0.839 0.894 0.000
## 244 G10 0.055 0.091 0.000 0.001 0.000
## 245 G11 0.000 0.001 0.073 0.156 0.000
## 246 G12 0.018 0.043 0.000 0.001 0.000
## 247 G13 0.999 1.000 0.000 0.001 0.000
## 248 G14 0.999 1.000 0.000 0.001 0.000
## 249 G15 0.998 1.000 0.000 0.001 0.000
## 250 G16 0.991 1.000 0.000 0.001 0.000
## 251 G17_rep 0.000 0.001 0.000 0.001 0.999
## 252 G18_rep 0.000 0.001 0.000 0.001 0.998
## 253 G19 0.000 0.002 0.301 0.425 0.000
## 254 G2 0.019 0.053 0.733 0.832 0.000
## 255 G20 0.000 0.001 0.000 0.001 0.000
## 256 G21 0.020 0.048 0.000 0.001 0.000
## 257 G22 0.034 0.068 0.000 0.001 0.000
## 258 G23 0.000 0.004 0.000 0.001 0.000
## 259 G24 0.000 0.001 0.000 0.001 0.000
## 260 G25 0.000 0.001 0.000 0.001 0.000
## 261 G26 0.000 0.001 0.000 0.001 0.000
## 262 G27 0.000 0.001 0.000 0.001 0.000
## 263 G28 0.027 0.057 0.000 0.001 0.000
## 264 G29 0.006 0.027 0.000 0.001 0.000
## 265 G3 0.977 1.000 0.000 0.002 0.000
## 266 G30 0.000 0.001 0.000 0.001 0.000
## 267 G31 0.000 0.001 0.000 0.001 0.000
## 268 G32 0.000 0.001 0.000 0.001 0.000
## 269 G33 0.000 0.001 0.000 0.009 0.000
## 270 G34 0.000 0.006 0.000 0.008 0.000
## 271 G35 0.000 0.001 0.053 0.143 0.000
## 272 G36 0.000 0.001 0.000 0.001 0.000
## 273 G37 0.000 0.001 0.000 0.001 0.000
## 274 G38 0.000 0.001 0.554 0.673 0.000
## 275 G39 0.028 0.070 0.000 0.023 0.000
## 276 G4 0.997 1.000 0.000 0.001 0.000
## 277 G40 0.000 0.001 0.027 0.087 0.000
## 278 G41_rep 0.000 0.001 0.000 0.001 0.000
## 279 G42 0.000 0.001 0.000 0.001 0.000
## 280 G43 0.000 0.001 0.996 1.000 0.000
## 281 G44 0.000 0.001 0.998 1.000 0.000
## 282 G45 0.000 0.001 0.991 1.000 0.000
## 283 G46 0.000 0.001 0.998 1.000 0.000
## 284 G47_rep 0.000 0.001 0.000 0.001 0.999
## 285 G48_rep 0.000 0.001 0.000 0.001 0.071
## 286 G49 0.000 0.001 0.000 0.014 0.000
## 287 G5_rep 0.000 0.001 0.311 0.378 0.621
## 288 G50 0.065 0.105 0.000 0.001 0.000
## 289 G52 0.000 0.001 0.207 0.304 0.000
## 290 G53 0.000 0.001 0.000 0.001 0.000
## 291 G54 0.000 0.001 0.000 0.001 0.000
## 292 G55 0.000 0.004 0.000 0.001 0.000
## 293 G56 0.000 0.001 0.000 0.001 0.000
## 294 G57 0.998 1.000 0.000 0.001 0.000
## 295 G58 0.999 1.000 0.000 0.001 0.000
## 296 G59 0.982 1.000 0.000 0.002 0.000
## 297 G6 0.000 0.001 0.053 0.114 0.000
## 298 G60 0.999 1.000 0.000 0.001 0.000
## 299 G61 0.000 0.001 0.000 0.001 0.000
## 300 G62 0.000 0.001 0.000 0.001 0.000
## 301 G63 0.000 0.009 0.121 0.209 0.000
## 302 G64 0.000 0.004 0.000 0.045 0.000
## 303 G65 0.000 0.001 0.000 0.001 0.000
## 304 G66 0.000 0.001 0.000 0.001 0.000
## 305 G67 0.000 0.001 0.000 0.002 0.000
## 306 G68 0.000 0.001 0.000 0.001 0.000
## 307 G69 0.000 0.014 0.000 0.001 0.000
## 308 G7_rep 0.000 0.001 0.000 0.001 0.998
## 309 G70 0.000 0.001 0.000 0.001 0.000
## 310 G71 0.000 0.001 0.000 0.001 0.033
## 311 G72 0.000 0.001 0.000 0.001 0.000
## 312 G73 0.999 1.000 0.000 0.001 0.000
## 313 G74 0.998 1.000 0.000 0.001 0.000
## 314 G76 0.999 1.000 0.000 0.001 0.000
## 315 G77 0.999 1.000 0.000 0.001 0.000
## 316 G78 0.000 0.001 0.827 0.918 0.000
## 317 G79 0.000 0.001 0.000 0.001 0.000
## 318 G8_rep 0.000 0.001 0.000 0.001 0.998
## 319 G80 0.009 0.040 0.000 0.003 0.000
## 320 G81 0.000 0.001 0.011 0.056 0.000
## 321 G82 0.000 0.001 0.000 0.001 0.000
## 322 G83 0.000 0.001 0.193 0.329 0.000
## 323 G84 0.000 0.018 0.000 0.002 0.000
## 324 G85 0.000 0.001 0.996 1.000 0.000
## 325 G86 0.000 0.001 0.996 1.000 0.000
## 326 G87 0.093 0.149 0.850 0.907 0.000
## 327 G88 0.000 0.001 0.991 1.000 0.000
## 328 G89 0.000 0.001 0.000 0.001 0.999
## 329 G9 0.000 0.001 0.163 0.256 0.000
## 330 G90 0.000 0.001 0.000 0.001 0.999
## 331 G92 0.000 0.001 0.000 0.001 0.999
## 332 G94 0.000 0.001 0.000 0.001 0.000
## 333 H1 0.000 0.005 0.946 0.985 0.013
## 334 H10 0.000 0.048 0.626 0.755 0.027
## 335 H11_rep 0.000 0.024 0.000 0.001 0.888
## 336 H12 0.000 0.001 0.195 0.294 0.000
## 337 H13 0.000 0.001 0.000 0.001 0.999
## 338 H14 0.000 0.001 0.000 0.001 0.999
## 339 H15 0.000 0.001 0.000 0.001 0.999
## 340 H16 0.000 0.001 0.000 0.001 0.999
## 341 H17 0.000 0.045 0.000 0.112 0.000
## 342 H18 0.000 0.028 0.000 0.001 0.000
## 343 H19 0.000 0.001 0.047 0.106 0.000
## 344 H2 0.000 0.001 0.817 0.914 0.033
## 345 H20 0.000 0.001 0.000 0.001 0.000
## 346 H21 0.000 0.001 0.140 0.227 0.000
## 347 H22 0.000 0.002 0.427 0.545 0.000
## 348 H23 0.012 0.043 0.144 0.239 0.000
## 349 H24 0.057 0.118 0.000 0.041 0.000
## 350 H25 0.000 0.001 0.000 0.001 0.000
## 351 H26 0.185 0.248 0.000 0.001 0.000
## 352 H27 0.000 0.001 0.000 0.001 0.000
## 353 H28 0.000 0.008 0.000 0.051 0.000
## 354 H29 0.000 0.001 0.000 0.001 0.999
## 355 H3 0.000 0.001 0.918 1.000 0.000
## 356 H30 0.000 0.001 0.000 0.001 0.999
## 357 H31 0.000 0.001 0.000 0.001 0.998
## 358 H32 0.000 0.001 0.000 0.001 0.999
## 359 H33 0.000 0.001 0.964 1.000 0.000
## 360 H34 0.000 0.001 0.911 0.971 0.027
## 361 H35 0.000 0.001 0.904 1.000 0.000
## 362 H36 0.000 0.001 0.998 1.000 0.000
## 363 H37 0.000 0.001 0.000 0.001 0.999
## 364 H38 0.000 0.001 0.000 0.001 0.999
## 365 H39 0.000 0.001 0.000 0.001 0.999
## 366 H4 0.000 0.001 0.000 0.001 0.999
## 367 H40 0.000 0.001 0.000 0.001 0.999
## 368 H41 0.000 0.001 0.000 0.001 0.000
## 369 H42 0.000 0.001 0.000 0.005 0.067
## 370 H43 0.000 0.001 0.000 0.001 0.999
## 371 H44 0.000 0.001 0.000 0.001 0.999
## 372 H45 0.000 0.001 0.000 0.001 0.999
## 373 H46 0.000 0.001 0.000 0.001 0.999
## 374 H47 0.000 0.001 0.876 0.974 0.000
## 375 H48 0.000 0.001 0.998 1.000 0.000
## 376 H49 0.000 0.001 0.996 1.000 0.000
## 377 H5 0.000 0.001 0.000 0.001 0.999
## 378 H50 0.000 0.001 0.994 1.000 0.000
## 379 H51 0.000 0.001 0.000 0.001 0.997
## 380 H52 0.000 0.001 0.000 0.001 0.999
## 381 H53 0.000 0.001 0.000 0.001 0.999
## 382 H54 0.000 0.001 0.000 0.001 0.999
## 383 H55 0.000 0.001 0.815 0.911 0.000
## 384 H56 0.000 0.001 0.993 1.000 0.000
## 385 H57 0.000 0.001 0.996 1.000 0.000
## 386 H58 0.000 0.001 0.993 1.000 0.000
## 387 H59 0.000 0.001 0.000 0.001 0.999
## 388 H6 0.000 0.001 0.000 0.001 0.999
## 389 H60 0.000 0.001 0.000 0.001 0.999
## 390 H62 0.000 0.001 0.000 0.001 0.999
## 391 H63 0.000 0.001 0.000 0.001 0.000
## 392 H64 0.000 0.001 0.604 0.721 0.000
## 393 H65_rep 0.000 0.001 0.000 0.001 0.999
## 394 H66_rep 0.000 0.001 0.000 0.001 0.999
## 395 H67 0.000 0.001 0.367 0.488 0.000
## 396 H68 0.000 0.001 0.413 0.533 0.000
## 397 H69_rep 0.000 0.005 0.000 0.020 0.977
## 398 H7 0.000 0.001 0.000 0.001 0.999
## 399 H70 0.000 0.001 0.000 0.020 0.000
## 400 H71 0.000 0.016 0.099 0.188 0.000
## 401 H72 0.000 0.001 0.000 0.001 0.000
## 402 H8_rep 0.000 0.001 0.000 0.001 0.999
## 403 H9 0.000 0.001 0.492 0.613 0.000
## 404 I01 0.000 0.002 0.000 0.001 0.990
## 405 I02 0.000 0.001 0.000 0.001 0.997
## 406 I03 0.000 0.001 0.000 0.001 0.999
## 407 I04 0.000 0.001 0.000 0.002 0.962
## 408 I05 0.000 0.001 0.000 0.003 0.981
## 409 I06 0.000 0.001 0.000 0.001 0.999
## 410 I07 0.000 0.001 0.000 0.001 0.999
## 411 I08 0.000 0.001 0.000 0.001 0.998
## 412 I09 0.000 0.001 0.000 0.001 0.999
## 413 I10 0.000 0.001 0.000 0.001 0.999
## 414 I11 0.000 0.001 0.000 0.001 0.999
## 415 I12 0.000 0.001 0.000 0.001 0.999
## 416 I13 0.000 0.001 0.000 0.001 0.999
## 417 I14 0.000 0.001 0.000 0.001 0.999
## 418 I15 0.000 0.001 0.000 0.001 0.999
## 419 I16 0.000 0.001 0.000 0.001 0.999
## 420 I17 0.000 0.001 0.000 0.001 0.998
## 421 I18 0.000 0.001 0.000 0.001 0.999
## 422 I19 0.000 0.001 0.000 0.001 0.999
## 423 I20 0.000 0.001 0.000 0.001 0.999
## 424 I21 0.000 0.001 0.000 0.001 0.999
## 425 I22 0.000 0.001 0.000 0.001 0.999
## 426 I23 0.000 0.001 0.000 0.001 0.999
## 427 I24 0.000 0.001 0.000 0.001 0.999
## 428 J14 0.000 0.009 0.000 0.013 0.000
## 429 J15 0.000 0.001 0.000 0.001 0.000
## 430 J16 0.000 0.001 0.000 0.001 0.000
## 431 J17 0.000 0.001 0.000 0.001 0.000
## 432 J18 0.000 0.016 0.000 0.001 0.000
## 433 J19 0.000 0.001 0.000 0.001 0.000
## 434 J20 0.000 0.001 0.000 0.001 0.000
## 435 J21 0.000 0.001 0.000 0.001 0.000
## 436 J22 0.000 0.001 0.000 0.001 0.000
## 437 J23 0.000 0.001 0.000 0.001 0.000
## 438 J24 0.000 0.001 0.000 0.001 0.000
## 439 J25 0.000 0.001 0.000 0.001 0.000
## 440 J26 0.000 0.001 0.000 0.001 0.000
## 441 J27 0.000 0.001 0.000 0.001 0.000
## 442 K1 0.000 0.001 0.000 0.001 0.000
## 443 K2 0.000 0.001 0.000 0.001 0.000
## 444 K3 0.000 0.001 0.000 0.001 0.000
## 445 K32 0.000 0.001 0.000 0.001 0.000
## 446 K33 0.000 0.001 0.000 0.004 0.000
## 447 K34 0.000 0.001 0.000 0.001 0.000
## 448 K4 0.000 0.001 0.000 0.001 0.000
## 449 K5 0.000 0.001 0.000 0.001 0.000
## 450 L1 0.000 0.001 0.000 0.001 0.000
## 451 L10 0.000 0.001 0.000 0.001 0.000
## 452 L11 0.000 0.001 0.000 0.001 0.000
## 453 L12 0.000 0.001 0.000 0.001 0.000
## 454 L13 0.000 0.002 0.000 0.003 0.000
## 455 L14 0.000 0.001 0.000 0.001 0.000
## 456 L15 0.000 0.001 0.000 0.001 0.000
## 457 L16 0.000 0.001 0.000 0.001 0.000
## 458 L17 0.000 0.001 0.000 0.001 0.000
## 459 L18_rep 0.000 0.001 0.000 0.001 0.000
## 460 L19 0.000 0.001 0.000 0.001 0.000
## 461 L2 0.000 0.001 0.000 0.002 0.000
## 462 L20 0.000 0.001 0.000 0.001 0.000
## 463 L21 0.000 0.001 0.000 0.001 0.000
## 464 L22 0.000 0.001 0.000 0.001 0.000
## 465 L23 0.000 0.001 0.000 0.001 0.000
## 466 L24 0.000 0.002 0.000 0.001 0.000
## 467 L26 0.000 0.001 0.000 0.001 0.000
## 468 L27 0.000 0.001 0.000 0.001 0.000
## 469 L28 0.000 0.001 0.000 0.001 0.000
## 470 L3 0.000 0.001 0.000 0.001 0.000
## 471 L4 0.000 0.001 0.000 0.001 0.000
## 472 L5 0.000 0.002 0.000 0.001 0.000
## 473 L6 0.000 0.001 0.000 0.001 0.000
## 474 L7 0.000 0.001 0.000 0.014 0.000
## 475 L8 0.000 0.001 0.000 0.001 0.000
## 476 L9_rep 0.000 0.001 0.000 0.001 0.000
## 477 N1 0.000 0.001 0.000 0.001 0.000
## 478 N10 0.000 0.001 0.000 0.003 0.000
## 479 N11 0.000 0.001 0.000 0.001 0.000
## 480 N12 0.000 0.001 0.000 0.001 0.000
## 481 N13 0.000 0.001 0.000 0.001 0.000
## 482 N14 0.000 0.001 0.000 0.001 0.000
## 483 N15 0.000 0.001 0.000 0.001 0.000
## 484 N16 0.000 0.001 0.000 0.001 0.000
## 485 N17 0.000 0.001 0.000 0.001 0.000
## 486 N18 0.000 0.001 0.000 0.001 0.000
## 487 N19 0.000 0.001 0.000 0.003 0.000
## 488 N20 0.000 0.001 0.000 0.001 0.000
## 489 N21 0.000 0.001 0.000 0.001 0.000
## 490 N24 0.000 0.001 0.000 0.001 0.000
## 491 N25 0.000 0.001 0.000 0.001 0.000
## 492 N26 0.000 0.001 0.000 0.003 0.000
## 493 N27 0.000 0.001 0.000 0.001 0.000
## 494 N28 0.000 0.001 0.000 0.001 0.000
## 495 N3 0.000 0.001 0.000 0.001 0.012
## 496 N4 0.000 0.001 0.000 0.001 0.000
## 497 N5 0.000 0.001 0.000 0.001 0.000
## 498 N6 0.000 0.001 0.000 0.001 0.000
## 499 N7 0.000 0.001 0.000 0.001 0.071
## 500 N8 0.000 0.001 0.000 0.002 0.000
## 501 N9 0.000 0.001 0.000 0.001 0.000
## 502 Q1 0.000 0.001 0.998 1.000 0.000
## 503 Q11 0.000 0.001 0.998 1.000 0.000
## 504 Q12 0.000 0.001 0.997 1.000 0.000
## 505 Q13 0.000 0.001 0.990 1.000 0.000
## 506 Q14 0.000 0.001 0.998 1.000 0.000
## 507 Q15 0.000 0.001 0.934 1.000 0.000
## 508 Q2 0.000 0.001 0.997 1.000 0.000
## 509 Q3 0.000 0.001 0.998 1.000 0.000
## 510 Q4 0.000 0.001 0.998 1.000 0.000
## 511 Q5 0.000 0.001 0.986 1.000 0.000
## 512 Q6 0.000 0.001 0.963 1.000 0.000
## 513 Q7 0.000 0.001 0.997 1.000 0.000
## 514 Q8 0.000 0.001 0.997 1.000 0.000
## 515 Q9 0.000 0.001 0.992 1.000 0.000
## 516 R10 0.000 0.001 0.000 0.001 0.000
## 517 R11 0.000 0.001 0.000 0.004 0.000
## 518 R12 0.000 0.001 0.000 0.001 0.000
## 519 R13 0.000 0.001 0.000 0.001 0.000
## 520 R14 0.000 0.001 0.000 0.001 0.000
## 521 R15 0.000 0.001 0.000 0.001 0.000
## 522 R16 0.000 0.001 0.000 0.001 0.000
## 523 R17 0.000 0.001 0.000 0.001 0.000
## 524 R18 0.000 0.001 0.000 0.001 0.000
## 525 R19 0.000 0.001 0.000 0.014 0.000
## 526 R2 0.000 0.001 0.000 0.001 0.000
## 527 R20 0.000 0.001 0.000 0.001 0.000
## 528 R3 0.000 0.001 0.000 0.012 0.000
## 529 R5 0.000 0.001 0.000 0.001 0.000
## 530 R6 0.000 0.001 0.000 0.001 0.000
## 531 R7 0.000 0.001 0.000 0.001 0.000
## 532 R9 0.000 0.001 0.000 0.001 0.000
## 533 S1 0.000 0.001 0.000 0.001 0.000
## 534 S11_rep 0.000 0.001 0.000 0.001 0.000
## 535 S12 0.000 0.001 0.000 0.001 0.000
## 536 S13 0.000 0.001 0.000 0.001 0.000
## 537 S15 0.000 0.001 0.000 0.001 0.000
## 538 S16 0.000 0.001 0.000 0.001 0.000
## 539 S17 0.000 0.001 0.000 0.001 0.000
## 540 S18 0.000 0.001 0.000 0.001 0.000
## 541 S19 0.000 0.001 0.000 0.001 0.000
## 542 S2 0.000 0.001 0.000 0.001 0.000
## 543 S20 0.000 0.001 0.000 0.001 0.000
## 544 S21 0.000 0.001 0.000 0.001 0.000
## 545 S22 0.000 0.001 0.000 0.001 0.000
## 546 S23 0.000 0.001 0.000 0.001 0.000
## 547 S24 0.000 0.001 0.000 0.001 0.000
## 548 S3 0.000 0.001 0.000 0.001 0.000
## 549 S4 0.000 0.001 0.000 0.001 0.000
## 550 S6 0.000 0.001 0.000 0.001 0.000
## 551 S7 0.000 0.001 0.000 0.001 0.000
## 552 S8 0.000 0.001 0.000 0.001 0.000
## 553 S9 0.000 0.001 0.000 0.001 0.000
## carinulata_H sublineata_L sublineata_H elongata carinata carinulata
## 1 0.001 0.000 0.001 1.000 0.000 0.000
## 2 0.001 0.000 0.001 1.000 0.000 0.000
## 3 0.001 0.000 0.001 1.000 0.000 0.000
## 4 0.078 0.000 0.028 0.936 0.000 0.058
## 5 0.001 0.000 0.001 1.000 0.000 0.000
## 6 0.001 0.000 0.001 1.000 0.000 0.000
## 7 0.001 0.000 0.001 1.000 0.000 0.000
## 8 0.001 0.000 0.001 1.000 0.000 0.000
## 9 0.001 0.000 0.001 1.000 0.000 0.000
## 10 0.001 0.000 0.001 1.000 0.000 0.000
## 11 0.001 0.000 0.001 1.000 0.000 0.000
## 12 0.001 0.000 0.001 1.000 0.000 0.000
## 13 0.001 0.000 0.001 1.000 0.000 0.000
## 14 0.079 0.000 0.001 0.942 0.000 0.058
## 15 0.001 0.000 0.001 1.000 0.000 0.000
## 16 0.001 0.000 0.001 1.000 0.000 0.000
## 17 0.001 0.000 0.001 1.000 0.000 0.000
## 18 0.001 0.000 0.001 1.000 0.000 0.000
## 19 0.001 0.000 0.001 1.000 0.000 0.000
## 20 0.001 0.000 0.001 1.000 0.000 0.000
## 21 0.001 0.000 0.001 1.000 0.000 0.000
## 22 0.001 0.000 0.001 1.000 0.000 0.000
## 23 0.001 0.000 0.001 1.000 0.000 0.000
## 24 0.001 0.000 0.001 1.000 0.000 0.000
## 25 0.001 0.000 0.001 1.000 0.000 0.000
## 26 0.001 0.000 0.001 1.000 0.000 0.000
## 27 0.001 0.000 0.001 1.000 0.000 0.000
## 28 0.001 0.000 0.001 1.000 0.000 0.000
## 29 0.001 0.000 0.001 1.000 0.000 0.000
## 30 0.001 0.000 0.001 1.000 0.000 0.000
## 31 0.001 0.000 0.001 1.000 0.000 0.000
## 32 0.001 0.000 0.001 1.000 0.000 0.000
## 33 0.001 0.000 0.001 1.000 0.000 0.000
## 34 0.001 0.000 0.001 1.000 0.000 0.000
## 35 0.001 0.000 0.001 1.000 0.000 0.000
## 36 0.001 0.000 0.001 1.000 0.000 0.000
## 37 0.001 0.000 0.001 1.000 0.000 0.000
## 38 0.001 0.000 0.001 1.000 0.000 0.000
## 39 0.001 0.000 0.001 1.000 0.000 0.000
## 40 0.001 0.000 0.001 1.000 0.000 0.000
## 41 0.001 0.000 0.001 1.000 0.000 0.000
## 42 0.001 0.000 0.001 1.000 0.000 0.000
## 43 0.001 0.000 0.001 1.000 0.000 0.000
## 44 0.001 0.000 0.001 1.000 0.000 0.000
## 45 0.001 0.000 0.001 1.000 0.000 0.000
## 46 0.001 0.000 0.001 1.000 0.000 0.000
## 47 0.001 0.000 0.001 1.000 0.000 0.000
## 48 0.001 0.000 0.001 1.000 0.000 0.000
## 49 0.001 0.000 0.001 1.000 0.000 0.000
## 50 0.014 0.000 0.004 0.997 0.000 0.002
## 51 0.001 0.000 0.001 1.000 0.000 0.000
## 52 0.139 0.000 0.002 0.885 0.000 0.114
## 53 0.009 0.000 0.001 0.999 0.000 0.001
## 54 0.001 0.000 0.001 1.000 0.000 0.000
## 55 0.001 0.000 0.001 1.000 0.000 0.000
## 56 0.001 0.000 0.001 1.000 0.000 0.000
## 57 0.001 0.000 0.001 1.000 0.000 0.000
## 58 0.001 0.000 0.001 1.000 0.000 0.000
## 59 0.001 0.000 0.001 1.000 0.000 0.000
## 60 0.001 0.000 0.001 1.000 0.000 0.000
## 61 0.001 0.000 0.001 1.000 0.000 0.000
## 62 0.001 0.000 0.001 1.000 0.000 0.000
## 63 0.001 0.000 0.001 1.000 0.000 0.000
## 64 0.001 0.000 0.001 1.000 0.000 0.000
## 65 0.001 0.000 0.001 1.000 0.000 0.000
## 66 0.001 0.000 0.001 1.000 0.000 0.000
## 67 0.001 0.000 0.001 1.000 0.000 0.000
## 68 0.001 0.000 0.001 1.000 0.000 0.000
## 69 0.001 0.000 0.001 1.000 0.000 0.000
## 70 0.001 0.000 0.001 1.000 0.000 0.000
## 71 0.001 0.000 0.001 1.000 0.000 0.000
## 72 0.001 0.000 0.001 1.000 0.000 0.000
## 73 0.001 0.000 0.001 1.000 0.000 0.000
## 74 0.001 0.000 0.001 0.999 0.000 0.000
## 75 0.001 0.000 0.001 1.000 0.000 0.000
## 76 0.001 0.000 0.001 1.000 0.000 0.000
## 77 1.000 0.000 0.001 0.000 0.000 1.000
## 78 1.000 0.000 0.001 0.000 0.000 1.000
## 79 1.000 0.000 0.001 0.000 0.000 1.000
## 80 1.000 0.000 0.001 0.000 0.000 1.000
## 81 1.000 0.000 0.001 0.000 0.000 1.000
## 82 1.000 0.000 0.001 0.000 0.000 1.000
## 83 1.000 0.000 0.001 0.000 0.000 1.000
## 84 1.000 0.000 0.001 0.000 0.000 1.000
## 85 1.000 0.000 0.001 0.000 0.000 1.000
## 86 1.000 0.000 0.001 0.000 0.000 1.000
## 87 1.000 0.000 0.001 0.000 0.000 1.000
## 88 1.000 0.000 0.001 0.000 0.000 1.000
## 89 1.000 0.000 0.001 0.000 0.000 1.000
## 90 1.000 0.000 0.001 0.000 0.000 1.000
## 91 1.000 0.000 0.001 0.000 0.000 1.000
## 92 1.000 0.000 0.001 0.000 0.000 1.000
## 93 1.000 0.000 0.001 0.000 0.000 1.000
## 94 1.000 0.000 0.001 0.000 0.000 1.000
## 95 0.001 0.000 0.002 0.247 0.752 0.000
## 96 1.000 0.000 0.001 0.000 0.000 1.000
## 97 0.001 0.000 0.008 0.000 0.999 0.000
## 98 1.000 0.000 0.001 0.000 0.000 1.000
## 99 1.000 0.000 0.001 0.000 0.000 1.000
## 100 1.000 0.000 0.001 0.000 0.000 1.000
## 101 1.000 0.000 0.001 0.000 0.000 1.000
## 102 1.000 0.000 0.001 0.000 0.000 1.000
## 103 1.000 0.000 0.001 0.000 0.000 1.000
## 104 1.000 0.000 0.001 0.000 0.000 1.000
## 105 1.000 0.000 0.001 0.000 0.000 1.000
## 106 1.000 0.000 0.001 0.000 0.000 1.000
## 107 1.000 0.000 0.001 0.000 0.000 1.000
## 108 1.000 0.000 0.001 0.000 0.000 1.000
## 109 1.000 0.000 0.001 0.000 0.000 1.000
## 110 1.000 0.000 0.001 0.000 0.000 1.000
## 111 1.000 0.000 0.001 0.000 0.000 1.000
## 112 1.000 0.000 0.001 0.000 0.000 1.000
## 113 1.000 0.000 0.001 0.000 0.000 1.000
## 114 1.000 0.000 0.001 0.000 0.000 1.000
## 115 1.000 0.000 0.001 0.000 0.000 1.000
## 116 1.000 0.000 0.001 0.000 0.000 1.000
## 117 1.000 0.000 0.001 0.000 0.000 1.000
## 118 1.000 0.000 0.001 0.000 0.000 1.000
## 119 1.000 0.000 0.001 0.000 0.000 1.000
## 120 1.000 0.000 0.001 0.000 0.000 1.000
## 121 1.000 0.000 0.001 0.000 0.000 1.000
## 122 1.000 0.000 0.001 0.000 0.000 1.000
## 123 1.000 0.000 0.001 0.000 0.000 1.000
## 124 1.000 0.000 0.001 0.000 0.000 1.000
## 125 1.000 0.000 0.001 0.000 0.000 1.000
## 126 1.000 0.000 0.001 0.000 0.000 1.000
## 127 1.000 0.000 0.001 0.000 0.000 1.000
## 128 1.000 0.000 0.001 0.000 0.000 1.000
## 129 1.000 0.000 0.001 0.000 0.000 1.000
## 130 1.000 0.000 0.001 0.000 0.000 1.000
## 131 1.000 0.000 0.001 0.000 0.000 1.000
## 132 1.000 0.000 0.001 0.000 0.000 1.000
## 133 1.000 0.000 0.001 0.000 0.000 1.000
## 134 1.000 0.000 0.001 0.000 0.000 1.000
## 135 1.000 0.000 0.001 0.000 0.000 1.000
## 136 1.000 0.000 0.001 0.000 0.000 1.000
## 137 1.000 0.000 0.001 0.000 0.000 1.000
## 138 1.000 0.000 0.001 0.000 0.000 1.000
## 139 1.000 0.000 0.001 0.000 0.000 1.000
## 140 1.000 0.000 0.001 0.000 0.000 1.000
## 141 1.000 0.000 0.001 0.000 0.000 1.000
## 142 1.000 0.000 0.001 0.000 0.000 1.000
## 143 1.000 0.000 0.001 0.000 0.000 1.000
## 144 1.000 0.000 0.001 0.000 0.000 1.000
## 145 1.000 0.000 0.001 0.000 0.000 1.000
## 146 1.000 0.000 0.001 0.000 0.000 1.000
## 147 1.000 0.000 0.001 0.000 0.000 1.000
## 148 1.000 0.000 0.001 0.000 0.000 1.000
## 149 1.000 0.000 0.001 0.000 0.000 1.000
## 150 1.000 0.000 0.001 0.000 0.000 1.000
## 151 1.000 0.000 0.001 0.000 0.000 1.000
## 152 1.000 0.000 0.001 0.000 0.000 1.000
## 153 1.000 0.000 0.001 0.000 0.000 1.000
## 154 1.000 0.000 0.001 0.000 0.000 1.000
## 155 1.000 0.000 0.001 0.000 0.000 1.000
## 156 1.000 0.000 0.001 0.000 0.000 1.000
## 157 1.000 0.000 0.001 0.000 0.000 1.000
## 158 1.000 0.000 0.001 0.000 0.000 1.000
## 159 1.000 0.000 0.001 0.000 0.000 1.000
## 160 1.000 0.000 0.001 0.000 0.000 1.000
## 161 1.000 0.000 0.001 0.000 0.000 1.000
## 162 1.000 0.000 0.001 0.000 0.000 1.000
## 163 1.000 0.000 0.001 0.000 0.000 1.000
## 164 1.000 0.000 0.001 0.000 0.000 1.000
## 165 1.000 0.000 0.006 0.000 0.001 0.999
## 166 1.000 0.000 0.001 0.000 0.000 1.000
## 167 1.000 0.000 0.001 0.000 0.000 1.000
## 168 1.000 0.000 0.003 0.000 0.000 0.999
## 169 1.000 0.000 0.001 0.000 0.000 1.000
## 170 1.000 0.000 0.001 0.000 0.000 1.000
## 171 1.000 0.000 0.001 0.000 0.000 1.000
## 172 1.000 0.000 0.001 0.000 0.000 1.000
## 173 1.000 0.000 0.001 0.000 0.000 1.000
## 174 1.000 0.000 0.001 0.000 0.000 1.000
## 175 1.000 0.000 0.001 0.000 0.000 1.000
## 176 0.001 0.000 0.002 0.000 1.000 0.000
## 177 0.001 0.000 0.002 0.000 1.000 0.000
## 178 0.001 0.000 0.057 0.000 0.987 0.000
## 179 0.001 0.000 0.002 0.000 1.000 0.000
## 180 0.001 0.000 0.001 0.000 1.000 0.000
## 181 0.001 0.000 0.002 0.000 1.000 0.000
## 182 1.000 0.000 0.001 0.000 0.000 1.000
## 183 1.000 0.000 0.001 0.000 0.000 1.000
## 184 1.000 0.000 0.001 0.000 0.000 1.000
## 185 1.000 0.000 0.001 0.000 0.000 1.000
## 186 0.001 0.000 0.080 0.000 0.970 0.000
## 187 0.001 0.000 0.003 0.000 0.999 0.000
## 188 0.001 0.000 0.001 0.000 1.000 0.000
## 189 0.001 0.000 0.001 0.000 1.000 0.000
## 190 0.001 0.000 0.003 0.000 0.999 0.000
## 191 0.001 0.000 0.012 0.000 0.998 0.000
## 192 0.001 0.000 0.003 0.000 0.999 0.000
## 193 0.001 0.000 0.004 0.000 0.999 0.000
## 194 1.000 0.000 0.001 0.000 0.000 1.000
## 195 1.000 0.000 0.001 0.000 0.000 1.000
## 196 1.000 0.000 0.001 0.000 0.000 1.000
## 197 1.000 0.000 0.009 0.000 0.000 0.998
## 198 1.000 0.000 0.001 0.000 0.000 1.000
## 199 0.001 0.000 0.001 1.000 0.000 0.000
## 200 0.001 0.000 0.001 0.000 1.000 0.000
## 201 0.001 0.000 0.002 0.000 0.999 0.000
## 202 0.001 0.000 0.001 0.000 1.000 0.000
## 203 0.001 0.000 0.001 0.000 1.000 0.000
## 204 1.000 0.000 0.001 0.000 0.000 1.000
## 205 1.000 0.000 0.001 0.000 0.000 1.000
## 206 1.000 0.000 0.001 0.000 0.000 1.000
## 207 1.000 0.000 0.001 0.000 0.000 1.000
## 208 0.001 0.000 0.001 0.000 1.000 0.000
## 209 0.001 0.000 0.033 0.000 0.995 0.000
## 210 0.001 0.000 0.001 1.000 0.000 0.000
## 211 0.001 0.000 0.001 1.000 0.000 0.000
## 212 0.001 0.000 0.002 0.000 1.000 0.000
## 213 0.001 0.000 0.008 0.004 0.995 0.000
## 214 0.001 0.000 0.002 0.000 1.000 0.000
## 215 0.001 0.000 0.002 0.000 1.000 0.000
## 216 1.000 0.000 0.001 0.000 0.000 1.000
## 217 1.000 0.000 0.001 0.000 0.000 1.000
## 218 1.000 0.000 0.001 0.000 0.000 1.000
## 219 1.000 0.000 0.001 0.000 0.000 1.000
## 220 0.001 0.997 1.000 0.000 0.000 0.000
## 221 0.001 0.999 1.000 0.000 0.000 0.000
## 222 0.001 0.998 1.000 0.000 0.000 0.000
## 223 0.001 0.869 0.935 0.025 0.071 0.000
## 224 0.001 0.000 0.009 0.000 0.999 0.000
## 225 0.001 0.000 0.008 0.000 0.999 0.000
## 226 0.001 0.000 0.001 0.000 1.000 0.000
## 227 0.002 0.000 0.001 0.000 0.999 0.000
## 228 0.001 0.995 1.000 0.000 0.000 0.000
## 229 0.001 0.837 0.911 0.037 0.087 0.000
## 230 0.001 0.000 0.001 1.000 0.000 0.000
## 231 0.001 0.000 0.003 0.000 0.999 0.000
## 232 0.024 0.000 0.022 0.003 0.990 0.004
## 233 0.001 0.000 0.002 0.000 0.999 0.000
## 234 0.001 0.000 0.054 0.000 0.988 0.000
## 235 1.000 0.000 0.001 0.000 0.000 1.000
## 236 0.001 0.000 0.003 0.000 0.999 0.000
## 237 1.000 0.000 0.001 0.000 0.000 1.000
## 238 0.001 0.459 0.581 0.000 0.480 0.000
## 239 0.001 0.996 1.000 0.000 0.001 0.000
## 240 0.019 0.768 0.865 0.031 0.148 0.003
## 241 0.001 0.874 0.946 0.000 0.087 0.000
## 242 0.001 0.615 0.729 0.002 0.326 0.000
## 243 0.001 0.000 0.002 0.133 0.867 0.000
## 244 0.001 0.909 0.945 0.072 0.000 0.000
## 245 0.001 0.843 0.927 0.000 0.112 0.000
## 246 0.001 0.957 0.982 0.029 0.000 0.000
## 247 0.001 0.000 0.001 1.000 0.000 0.000
## 248 0.001 0.000 0.001 1.000 0.000 0.000
## 249 0.001 0.000 0.001 1.000 0.000 0.000
## 250 0.001 0.000 0.006 0.999 0.000 0.000
## 251 1.000 0.000 0.001 0.000 0.000 1.000
## 252 1.000 0.000 0.001 0.000 0.000 1.000
## 253 0.001 0.575 0.699 0.000 0.362 0.000
## 254 0.001 0.135 0.230 0.035 0.784 0.000
## 255 0.001 0.997 1.000 0.000 0.000 0.000
## 256 0.001 0.952 0.980 0.033 0.000 0.000
## 257 0.001 0.932 0.966 0.050 0.000 0.000
## 258 0.017 0.982 1.000 0.001 0.000 0.004
## 259 0.001 0.999 1.000 0.000 0.000 0.000
## 260 0.001 0.999 1.000 0.000 0.000 0.000
## 261 0.001 0.999 1.000 0.000 0.000 0.000
## 262 0.001 0.998 1.000 0.000 0.000 0.000
## 263 0.001 0.943 0.973 0.041 0.000 0.000
## 264 0.001 0.972 0.993 0.016 0.000 0.000
## 265 0.001 0.000 0.022 0.996 0.000 0.000
## 266 0.001 0.998 1.000 0.000 0.000 0.000
## 267 0.001 0.998 1.000 0.000 0.000 0.000
## 268 0.001 0.999 1.000 0.000 0.000 0.000
## 269 0.001 0.991 1.000 0.000 0.001 0.000
## 270 0.002 0.989 1.000 0.001 0.001 0.000
## 271 0.001 0.857 0.947 0.000 0.094 0.000
## 272 0.001 0.999 1.000 0.000 0.000 0.000
## 273 0.001 0.999 1.000 0.000 0.000 0.000
## 274 0.001 0.327 0.446 0.000 0.614 0.000
## 275 0.002 0.924 0.969 0.048 0.003 0.000
## 276 0.001 0.000 0.001 1.000 0.000 0.000
## 277 0.001 0.913 0.973 0.000 0.055 0.000
## 278 0.015 0.984 1.000 0.000 0.000 0.004
## 279 0.001 0.998 1.000 0.000 0.000 0.000
## 280 0.001 0.000 0.002 0.000 0.999 0.000
## 281 0.001 0.000 0.001 0.000 1.000 0.000
## 282 0.001 0.000 0.008 0.000 0.999 0.000
## 283 0.001 0.000 0.001 0.000 1.000 0.000
## 284 1.000 0.000 0.001 0.000 0.000 1.000
## 285 0.112 0.888 0.929 0.000 0.000 0.091
## 286 0.001 0.986 1.000 0.000 0.002 0.000
## 287 0.683 0.000 0.023 0.000 0.345 0.652
## 288 0.001 0.895 0.935 0.084 0.000 0.000
## 289 0.001 0.696 0.793 0.000 0.254 0.000
## 290 0.001 0.999 1.000 0.000 0.000 0.000
## 291 0.001 0.998 1.000 0.000 0.000 0.000
## 292 0.017 0.983 1.000 0.000 0.000 0.003
## 293 0.001 0.998 1.000 0.000 0.000 0.000
## 294 0.001 0.000 0.001 1.000 0.000 0.000
## 295 0.001 0.000 0.001 1.000 0.000 0.000
## 296 0.007 0.000 0.015 0.997 0.000 0.001
## 297 0.001 0.886 0.947 0.000 0.082 0.000
## 298 0.001 0.000 0.001 1.000 0.000 0.000
## 299 0.001 0.998 1.000 0.000 0.000 0.000
## 300 0.001 0.998 1.000 0.000 0.000 0.000
## 301 0.001 0.790 0.877 0.001 0.164 0.000
## 302 0.001 0.955 1.000 0.001 0.010 0.000
## 303 0.001 0.998 1.000 0.000 0.000 0.000
## 304 0.001 0.998 1.000 0.000 0.000 0.000
## 305 0.001 0.996 1.000 0.000 0.001 0.000
## 306 0.001 0.999 1.000 0.000 0.000 0.000
## 307 0.001 0.985 1.000 0.003 0.000 0.000
## 308 1.000 0.000 0.001 0.000 0.000 1.000
## 309 0.001 0.999 1.000 0.000 0.000 0.000
## 310 0.066 0.934 0.967 0.000 0.000 0.049
## 311 0.001 0.999 1.000 0.000 0.000 0.000
## 312 0.001 0.000 0.001 1.000 0.000 0.000
## 313 0.001 0.000 0.001 1.000 0.000 0.000
## 314 0.001 0.000 0.001 1.000 0.000 0.000
## 315 0.001 0.000 0.001 1.000 0.000 0.000
## 316 0.001 0.082 0.172 0.000 0.875 0.000
## 317 0.001 0.996 1.000 0.000 0.000 0.000
## 318 1.000 0.000 0.001 0.000 0.000 1.000
## 319 0.001 0.958 0.990 0.024 0.001 0.000
## 320 0.001 0.944 0.989 0.000 0.032 0.000
## 321 0.001 0.998 1.000 0.000 0.000 0.000
## 322 0.001 0.671 0.806 0.000 0.259 0.000
## 323 0.001 0.981 1.000 0.007 0.000 0.000
## 324 0.001 0.000 0.003 0.000 0.999 0.000
## 325 0.001 0.000 0.002 0.000 0.999 0.000
## 326 0.001 0.000 0.001 0.120 0.880 0.000
## 327 0.001 0.000 0.008 0.000 0.999 0.000
## 328 1.000 0.000 0.001 0.000 0.000 1.000
## 329 0.001 0.744 0.837 0.000 0.208 0.000
## 330 1.000 0.000 0.001 0.000 0.000 1.000
## 331 1.000 0.000 0.001 0.000 0.000 1.000
## 332 0.001 0.998 1.000 0.000 0.000 0.000
## 333 0.047 0.000 0.019 0.001 0.967 0.029
## 334 0.073 0.183 0.307 0.014 0.692 0.050
## 335 0.926 0.066 0.109 0.004 0.000 0.908
## 336 0.001 0.706 0.805 0.000 0.242 0.000
## 337 1.000 0.000 0.001 0.000 0.000 1.000
## 338 1.000 0.000 0.001 0.000 0.000 1.000
## 339 1.000 0.000 0.001 0.000 0.000 1.000
## 340 1.000 0.000 0.001 0.000 0.000 1.000
## 341 0.001 0.877 0.958 0.019 0.063 0.000
## 342 0.005 0.972 1.000 0.014 0.000 0.001
## 343 0.001 0.893 0.953 0.000 0.075 0.000
## 344 0.076 0.032 0.130 0.000 0.866 0.054
## 345 0.001 0.998 1.000 0.000 0.000 0.000
## 346 0.001 0.773 0.860 0.000 0.183 0.000
## 347 0.001 0.454 0.572 0.000 0.486 0.000
## 348 0.001 0.736 0.828 0.026 0.190 0.000
## 349 0.010 0.869 0.937 0.086 0.006 0.001
## 350 0.001 0.998 1.000 0.000 0.000 0.000
## 351 0.007 0.751 0.814 0.216 0.000 0.001
## 352 0.008 0.991 1.000 0.000 0.000 0.001
## 353 0.012 0.948 1.000 0.001 0.018 0.002
## 354 1.000 0.000 0.001 0.000 0.000 1.000
## 355 0.004 0.000 0.082 0.000 0.970 0.001
## 356 1.000 0.000 0.001 0.000 0.000 1.000
## 357 1.000 0.000 0.001 0.000 0.000 1.000
## 358 1.000 0.000 0.001 0.000 0.000 1.000
## 359 0.001 0.000 0.035 0.000 0.995 0.000
## 360 0.066 0.000 0.042 0.000 0.948 0.045
## 361 0.001 0.000 0.095 0.000 0.952 0.000
## 362 0.001 0.000 0.001 0.000 1.000 0.000
## 363 1.000 0.000 0.001 0.000 0.000 1.000
## 364 1.000 0.000 0.001 0.000 0.000 1.000
## 365 1.000 0.000 0.001 0.000 0.000 1.000
## 366 1.000 0.000 0.001 0.000 0.000 1.000
## 367 1.000 0.000 0.001 0.000 0.000 1.000
## 368 0.001 0.998 1.000 0.000 0.000 0.000
## 369 0.118 0.879 0.932 0.000 0.001 0.091
## 370 1.000 0.000 0.001 0.000 0.000 1.000
## 371 1.000 0.000 0.001 0.000 0.000 1.000
## 372 1.000 0.000 0.001 0.000 0.000 1.000
## 373 1.000 0.000 0.001 0.000 0.000 1.000
## 374 0.001 0.026 0.123 0.000 0.926 0.000
## 375 0.001 0.000 0.001 0.000 1.000 0.000
## 376 0.001 0.000 0.003 0.000 0.999 0.000
## 377 1.000 0.000 0.001 0.000 0.000 1.000
## 378 0.001 0.000 0.003 0.000 0.999 0.000
## 379 1.000 0.000 0.001 0.000 0.000 1.000
## 380 1.000 0.000 0.001 0.000 0.000 1.000
## 381 1.000 0.000 0.001 0.000 0.000 1.000
## 382 1.000 0.000 0.001 0.000 0.000 1.000
## 383 0.001 0.088 0.185 0.000 0.865 0.000
## 384 0.004 0.000 0.002 0.000 0.999 0.001
## 385 0.001 0.000 0.003 0.000 0.999 0.000
## 386 0.001 0.000 0.006 0.000 0.999 0.000
## 387 1.000 0.000 0.001 0.000 0.000 1.000
## 388 1.000 0.000 0.001 0.000 0.000 1.000
## 389 1.000 0.000 0.001 0.000 0.000 1.000
## 390 1.000 0.000 0.001 0.000 0.000 1.000
## 391 0.001 0.999 1.000 0.000 0.000 0.000
## 392 0.001 0.279 0.396 0.000 0.662 0.000
## 393 1.000 0.000 0.001 0.000 0.000 1.000
## 394 1.000 0.000 0.001 0.000 0.000 1.000
## 395 0.001 0.512 0.633 0.000 0.427 0.000
## 396 0.001 0.467 0.587 0.000 0.473 0.000
## 397 0.996 0.000 0.019 0.001 0.006 0.987
## 398 1.000 0.000 0.001 0.000 0.000 1.000
## 399 0.001 0.979 1.000 0.000 0.003 0.000
## 400 0.001 0.810 0.898 0.002 0.142 0.000
## 401 0.001 0.998 1.000 0.000 0.000 0.000
## 402 1.000 0.000 0.001 0.000 0.000 1.000
## 403 0.001 0.387 0.507 0.000 0.553 0.000
## 404 1.000 0.000 0.010 0.000 0.000 0.997
## 405 1.000 0.000 0.002 0.000 0.000 1.000
## 406 1.000 0.000 0.001 0.000 0.000 1.000
## 407 0.983 0.016 0.038 0.000 0.000 0.973
## 408 0.999 0.000 0.019 0.000 0.000 0.990
## 409 1.000 0.000 0.001 0.000 0.000 1.000
## 410 1.000 0.000 0.001 0.000 0.000 1.000
## 411 1.000 0.000 0.001 0.000 0.000 1.000
## 412 1.000 0.000 0.001 0.000 0.000 1.000
## 413 1.000 0.000 0.001 0.000 0.000 1.000
## 414 1.000 0.000 0.001 0.000 0.000 1.000
## 415 1.000 0.000 0.001 0.000 0.000 1.000
## 416 1.000 0.000 0.001 0.000 0.000 1.000
## 417 1.000 0.000 0.001 0.000 0.000 1.000
## 418 1.000 0.000 0.001 0.000 0.000 1.000
## 419 1.000 0.000 0.001 0.000 0.000 1.000
## 420 1.000 0.000 0.001 0.000 0.000 1.000
## 421 1.000 0.000 0.001 0.000 0.000 1.000
## 422 1.000 0.000 0.001 0.000 0.000 1.000
## 423 1.000 0.000 0.001 0.000 0.000 1.000
## 424 1.000 0.000 0.001 0.000 0.000 1.000
## 425 1.000 0.000 0.001 0.000 0.000 1.000
## 426 1.000 0.000 0.001 0.000 0.000 1.000
## 427 1.000 0.000 0.001 0.000 0.000 1.000
## 428 0.001 0.985 1.000 0.001 0.002 0.000
## 429 0.001 0.998 1.000 0.000 0.000 0.000
## 430 0.001 0.999 1.000 0.000 0.000 0.000
## 431 0.001 0.998 1.000 0.000 0.000 0.000
## 432 0.001 0.984 1.000 0.003 0.000 0.000
## 433 0.001 0.999 1.000 0.000 0.000 0.000
## 434 0.001 0.999 1.000 0.000 0.000 0.000
## 435 0.001 0.998 1.000 0.000 0.000 0.000
## 436 0.001 0.998 1.000 0.000 0.000 0.000
## 437 0.001 0.999 1.000 0.000 0.000 0.000
## 438 0.001 0.999 1.000 0.000 0.000 0.000
## 439 0.001 0.999 1.000 0.000 0.000 0.000
## 440 0.001 0.999 1.000 0.000 0.000 0.000
## 441 0.001 0.999 1.000 0.000 0.000 0.000
## 442 0.001 0.999 1.000 0.000 0.000 0.000
## 443 0.001 0.998 1.000 0.000 0.000 0.000
## 444 0.001 0.998 1.000 0.000 0.000 0.000
## 445 0.001 0.999 1.000 0.000 0.000 0.000
## 446 0.001 0.995 1.000 0.000 0.001 0.000
## 447 0.001 0.999 1.000 0.000 0.000 0.000
## 448 0.001 0.999 1.000 0.000 0.000 0.000
## 449 0.001 0.998 1.000 0.000 0.000 0.000
## 450 0.001 0.999 1.000 0.000 0.000 0.000
## 451 0.001 0.998 1.000 0.000 0.000 0.000
## 452 0.001 0.999 1.000 0.000 0.000 0.000
## 453 0.001 0.999 1.000 0.000 0.000 0.000
## 454 0.001 0.995 1.000 0.000 0.000 0.000
## 455 0.001 0.998 1.000 0.000 0.000 0.000
## 456 0.001 0.999 1.000 0.000 0.000 0.000
## 457 0.001 0.999 1.000 0.000 0.000 0.000
## 458 0.001 0.999 1.000 0.000 0.000 0.000
## 459 0.001 0.998 1.000 0.000 0.000 0.000
## 460 0.001 0.999 1.000 0.000 0.000 0.000
## 461 0.001 0.997 1.000 0.000 0.000 0.000
## 462 0.001 0.999 1.000 0.000 0.000 0.000
## 463 0.001 0.999 1.000 0.000 0.000 0.000
## 464 0.001 0.999 1.000 0.000 0.000 0.000
## 465 0.001 0.999 1.000 0.000 0.000 0.000
## 466 0.001 0.997 1.000 0.000 0.000 0.000
## 467 0.001 0.998 1.000 0.000 0.000 0.000
## 468 0.001 0.999 1.000 0.000 0.000 0.000
## 469 0.001 0.998 1.000 0.000 0.000 0.000
## 470 0.001 0.999 1.000 0.000 0.000 0.000
## 471 0.001 0.999 1.000 0.000 0.000 0.000
## 472 0.002 0.994 1.000 0.000 0.000 0.000
## 473 0.001 0.998 1.000 0.000 0.000 0.000
## 474 0.001 0.986 1.000 0.000 0.002 0.000
## 475 0.001 0.999 1.000 0.000 0.000 0.000
## 476 0.001 0.999 1.000 0.000 0.000 0.000
## 477 0.001 0.998 1.000 0.000 0.000 0.000
## 478 0.007 0.990 1.000 0.000 0.001 0.001
## 479 0.002 0.996 1.000 0.000 0.000 0.000
## 480 0.001 0.999 1.000 0.000 0.000 0.000
## 481 0.001 0.999 1.000 0.000 0.000 0.000
## 482 0.001 0.998 1.000 0.000 0.000 0.000
## 483 0.001 0.999 1.000 0.000 0.000 0.000
## 484 0.001 0.999 1.000 0.000 0.000 0.000
## 485 0.001 0.999 1.000 0.000 0.000 0.000
## 486 0.014 0.985 1.000 0.000 0.000 0.003
## 487 0.001 0.996 1.000 0.000 0.000 0.000
## 488 0.001 0.998 1.000 0.000 0.000 0.000
## 489 0.001 0.998 1.000 0.000 0.000 0.000
## 490 0.001 0.999 1.000 0.000 0.000 0.000
## 491 0.001 0.999 1.000 0.000 0.000 0.000
## 492 0.007 0.990 1.000 0.000 0.001 0.001
## 493 0.011 0.989 1.000 0.000 0.000 0.002
## 494 0.001 0.999 1.000 0.000 0.000 0.000
## 495 0.039 0.961 0.987 0.000 0.000 0.025
## 496 0.001 0.999 1.000 0.000 0.000 0.000
## 497 0.001 0.999 1.000 0.000 0.000 0.000
## 498 0.001 0.999 1.000 0.000 0.000 0.000
## 499 0.120 0.880 0.929 0.000 0.000 0.094
## 500 0.001 0.997 1.000 0.000 0.000 0.000
## 501 0.001 0.998 1.000 0.000 0.000 0.000
## 502 0.001 0.000 0.001 0.000 1.000 0.000
## 503 0.001 0.000 0.001 0.000 1.000 0.000
## 504 0.001 0.000 0.002 0.000 1.000 0.000
## 505 0.001 0.000 0.009 0.000 0.999 0.000
## 506 0.001 0.000 0.001 0.000 1.000 0.000
## 507 0.001 0.000 0.066 0.000 0.982 0.000
## 508 0.001 0.000 0.002 0.000 1.000 0.000
## 509 0.001 0.000 0.001 0.000 1.000 0.000
## 510 0.001 0.000 0.001 0.000 1.000 0.000
## 511 0.001 0.000 0.014 0.000 0.998 0.000
## 512 0.001 0.000 0.037 0.000 0.994 0.000
## 513 0.001 0.000 0.002 0.000 1.000 0.000
## 514 0.001 0.000 0.002 0.000 1.000 0.000
## 515 0.007 0.000 0.001 0.000 0.999 0.001
## 516 0.001 0.999 1.000 0.000 0.000 0.000
## 517 0.001 0.993 1.000 0.000 0.001 0.000
## 518 0.001 0.998 1.000 0.000 0.000 0.000
## 519 0.001 0.999 1.000 0.000 0.000 0.000
## 520 0.001 0.999 1.000 0.000 0.000 0.000
## 521 0.001 0.998 1.000 0.000 0.000 0.000
## 522 0.001 0.999 1.000 0.000 0.000 0.000
## 523 0.001 0.999 1.000 0.000 0.000 0.000
## 524 0.001 0.999 1.000 0.000 0.000 0.000
## 525 0.011 0.983 1.000 0.000 0.002 0.002
## 526 0.001 0.999 1.000 0.000 0.000 0.000
## 527 0.001 0.998 1.000 0.000 0.000 0.000
## 528 0.001 0.988 1.000 0.000 0.001 0.000
## 529 0.001 0.999 1.000 0.000 0.000 0.000
## 530 0.001 0.998 1.000 0.000 0.000 0.000
## 531 0.001 0.999 1.000 0.000 0.000 0.000
## 532 0.001 0.999 1.000 0.000 0.000 0.000
## 533 0.001 0.999 1.000 0.000 0.000 0.000
## 534 0.001 0.999 1.000 0.000 0.000 0.000
## 535 0.009 0.990 1.000 0.000 0.000 0.001
## 536 0.001 0.999 1.000 0.000 0.000 0.000
## 537 0.001 0.999 1.000 0.000 0.000 0.000
## 538 0.001 0.999 1.000 0.000 0.000 0.000
## 539 0.001 0.999 1.000 0.000 0.000 0.000
## 540 0.001 0.998 1.000 0.000 0.000 0.000
## 541 0.001 0.998 1.000 0.000 0.000 0.000
## 542 0.001 0.999 1.000 0.000 0.000 0.000
## 543 0.001 0.998 1.000 0.000 0.000 0.000
## 544 0.001 0.999 1.000 0.000 0.000 0.000
## 545 0.005 0.994 1.000 0.000 0.000 0.001
## 546 0.001 0.999 1.000 0.000 0.000 0.000
## 547 0.001 0.998 1.000 0.000 0.000 0.000
## 548 0.001 0.998 1.000 0.000 0.000 0.000
## 549 0.001 0.999 1.000 0.000 0.000 0.000
## 550 0.001 0.999 1.000 0.000 0.000 0.000
## 551 0.001 0.999 1.000 0.000 0.000 0.000
## 552 0.001 0.999 1.000 0.000 0.000 0.000
## 553 0.001 0.999 1.000 0.000 0.000 0.000
## sublineata popID
## 1 0.000 38CR
## 2 0.000 41CR
## 3 0.000 41CR
## 4 0.006 41CR
## 5 0.000 41CR
## 6 0.000 43GR
## 7 0.000 43GR
## 8 0.000 43GR
## 9 0.000 38CR
## 10 0.000 43GR
## 11 0.000 44GR
## 12 0.000 44GR
## 13 0.000 44GR
## 14 0.000 44GR
## 15 0.000 44GR
## 16 0.000 38CR
## 17 0.000 43GR
## 18 0.000 43GR
## 19 0.000 43GR
## 20 0.000 44GR
## 21 0.000 44GR
## 22 0.000 44GR
## 23 0.000 38CR
## 24 0.000 44GR
## 25 0.000 41CR
## 26 0.000 41CR
## 27 0.000 41CR
## 28 0.000 41CR
## 29 0.000 37CR
## 30 0.000 37CR
## 31 0.000 37CR
## 32 0.000 38CR
## 33 0.000 39CR
## 34 0.000 38CR
## 35 0.000 38CR
## 36 0.000 38CR
## 37 0.000 39CR
## 38 0.000 39CR
## 39 0.000 39CR
## 40 0.000 39CR
## 41 0.000 41CR
## 42 0.000 41CR
## 43 0.000 41CR
## 44 0.000 39CR
## 45 0.000 41CR
## 46 0.000 43GR
## 47 0.000 43GR
## 48 0.000 43GR
## 49 0.000 43GR
## 50 0.001 44GR
## 51 0.000 39CR
## 52 0.000 37CR
## 53 0.000 37CR
## 54 0.000 37CR
## 55 0.000 38CR
## 56 0.000 38CR
## 57 0.000 38CR
## 58 0.000 39CR
## 59 0.000 39CR
## 60 0.000 39CR
## 61 0.000 39CR
## 62 0.000 39CR
## 63 0.000 41CR
## 64 0.000 41CR
## 65 0.000 41CR
## 66 0.000 41CR
## 67 0.000 43GR
## 68 0.000 43GR
## 69 0.000 43GR
## 70 0.000 43GR
## 71 0.000 44GR
## 72 0.000 44GR
## 73 0.000 44GR
## 74 0.000 44GR
## 75 0.000 44GR
## 76 0.000 44GR
## 77 0.000 1WY
## 78 0.000 32UT
## 79 0.000 32UT
## 80 0.000 32UT
## 81 0.000 1WY
## 82 0.000 1WY
## 83 0.000 34UT
## 84 0.000 34UT
## 85 0.000 34UT
## 86 0.000 34UT
## 87 0.000 32UT
## 88 0.000 32UT
## 89 0.000 32UT
## 90 0.000 32UT
## 91 0.000 1WY
## 92 0.000 1WY
## 93 0.000 1WY
## 94 0.000 1WY
## 95 0.000 15TX
## 96 0.000 1WY
## 97 0.001 15TX
## 98 0.000 32UT
## 99 0.000 32UT
## 100 0.000 32UT
## 101 0.000 32UT
## 102 0.000 1WY
## 103 0.000 1WY
## 104 0.000 1WY
## 105 0.000 1WY
## 106 0.000 34UT
## 107 0.000 1WY
## 108 0.000 34UT
## 109 0.000 34UT
## 110 0.000 34UT
## 111 0.000 32UT
## 112 0.000 32UT
## 113 0.000 32UT
## 114 0.000 32UT
## 115 0.000 1WY
## 116 0.000 1WY
## 117 0.000 1WY
## 118 0.000 34UT
## 119 0.000 1WY
## 120 0.000 34UT
## 121 0.000 34UT
## 122 0.000 34UT
## 123 0.000 34UT
## 124 0.000 32UT
## 125 0.000 32UT
## 126 0.000 32UT
## 127 0.000 32UT
## 128 0.000 12AZ
## 129 0.000 12AZ
## 130 0.000 33NV
## 131 0.000 33NV
## 132 0.000 33NV
## 133 0.000 33NV
## 134 0.000 12AZ
## 135 0.000 12AZ
## 136 0.000 12AZ
## 137 0.000 11CO
## 138 0.000 34UT
## 139 0.000 11CO
## 140 0.000 33NV
## 141 0.000 33NV
## 142 0.000 12AZ
## 143 0.000 12AZ
## 144 0.000 34UT
## 145 0.000 11CO
## 146 0.000 11CO
## 147 0.000 33NV
## 148 0.000 33NV
## 149 0.000 33NV
## 150 0.000 32UT
## 151 0.000 34UT
## 152 0.000 11CO
## 153 0.000 11CO
## 154 0.000 31NV
## 155 0.000 31NV
## 156 0.000 11CO
## 157 0.000 31NV
## 158 0.000 31NV
## 159 0.000 31NV
## 160 0.000 31NV
## 161 0.000 12AZ
## 162 0.000 12AZ
## 163 0.000 12AZ
## 164 0.000 12AZ
## 165 0.001 11CO
## 166 0.000 31NV
## 167 0.000 11CO
## 168 0.000 11CO
## 169 0.000 11CO
## 170 0.000 12AZ
## 171 0.000 12AZ
## 172 0.000 5CO
## 173 0.000 5CO
## 174 0.000 5CO
## 175 0.000 5CO
## 176 0.000 6KS
## 177 0.000 6KS
## 178 0.013 8OK
## 179 0.000 8OK
## 180 0.000 8OK
## 181 0.000 8OK
## 182 0.000 5CO
## 183 0.000 5CO
## 184 0.000 5CO
## 185 0.000 12AZ
## 186 0.030 6KS
## 187 0.001 6KS
## 188 0.000 6KS
## 189 0.000 6KS
## 190 0.000 8OK
## 191 0.002 8OK
## 192 0.001 8OK
## 193 0.001 8OK
## 194 0.000 5CO
## 195 0.000 12AZ
## 196 0.000 5CO
## 197 0.001 5CO
## 198 0.000 5CO
## 199 0.000 16TX
## 200 0.000 8OK
## 201 0.000 8OK
## 202 0.000 8OK
## 203 0.000 8OK
## 204 0.000 5CO
## 205 0.000 5CO
## 206 0.000 5CO
## 207 0.000 5CO
## 208 0.000 6KS
## 209 0.005 6KS
## 210 0.000 16TX
## 211 0.000 16TX
## 212 0.000 8OK
## 213 0.001 8OK
## 214 0.000 8OK
## 215 0.000 8OK
## 216 0.000 5CO
## 217 0.000 5CO
## 218 0.000 5CO
## 219 0.000 5CO
## 220 1.000 27NM
## 221 1.000 27NM
## 222 1.000 27NM
## 223 0.904 27NM
## 224 0.001 8OK
## 225 0.001 8OK
## 226 0.000 8OK
## 227 0.000 8OK
## 228 0.999 26NM
## 229 0.876 26NM
## 230 0.000 15TX
## 231 0.000 15TX
## 232 0.003 15TX
## 233 0.000 15TX
## 234 0.012 28NM
## 235 0.000 11CO
## 236 0.001 28NM
## 237 0.000 28NM
## 238 0.520 28NM
## 239 0.999 26NM
## 240 0.819 26NM
## 241 0.913 26NM
## 242 0.672 26NM
## 243 0.000 15TX
## 244 0.927 26NM
## 245 0.888 26NM
## 246 0.970 26NM
## 247 0.000 16TX
## 248 0.000 16TX
## 249 0.000 16TX
## 250 0.001 16TX
## 251 0.000 28NM
## 252 0.000 28NM
## 253 0.638 27NM
## 254 0.181 15TX
## 255 1.000 27NM
## 256 0.967 27NM
## 257 0.950 27NM
## 258 0.996 20NM
## 259 1.000 20NM
## 260 1.000 20NM
## 261 1.000 20NM
## 262 1.000 27NM
## 263 0.959 27NM
## 264 0.984 27NM
## 265 0.003 16TX
## 266 1.000 27NM
## 267 1.000 21NM
## 268 1.000 21NM
## 269 0.999 21NM
## 270 0.998 21NM
## 271 0.905 20NM
## 272 1.000 20NM
## 273 1.000 20NM
## 274 0.386 20NM
## 275 0.949 21NM
## 276 0.000 16TX
## 277 0.945 21NM
## 278 0.996 21NM
## 279 1.000 21NM
## 280 0.000 15TX
## 281 0.000 15TX
## 282 0.001 15TX
## 283 0.000 15TX
## 284 0.000 6KS
## 285 0.909 6KS
## 286 0.998 20NM
## 287 0.003 28NM
## 288 0.916 20NM
## 289 0.745 20NM
## 290 1.000 18TX
## 291 1.000 18TX
## 292 0.996 18TX
## 293 1.000 18TX
## 294 0.000 16TX
## 295 0.000 16TX
## 296 0.002 16TX
## 297 0.918 28NM
## 298 0.000 16TX
## 299 1.000 20NM
## 300 1.000 20NM
## 301 0.835 20NM
## 302 0.990 20NM
## 303 1.000 18TX
## 304 1.000 18TX
## 305 0.999 18TX
## 306 1.000 18TX
## 307 0.997 20NM
## 308 0.000 28NM
## 309 1.000 20NM
## 310 0.951 18TX
## 311 1.000 18TX
## 312 0.000 16TX
## 313 0.000 16TX
## 314 0.000 16TX
## 315 0.000 16TX
## 316 0.125 16TX
## 317 0.999 27NM
## 318 0.000 28NM
## 319 0.975 27NM
## 320 0.968 27NM
## 321 1.000 27NM
## 322 0.741 21NM
## 323 0.992 21NM
## 324 0.000 15TX
## 325 0.000 15TX
## 326 0.000 15TX
## 327 0.001 15TX
## 328 0.000 2CO
## 329 0.792 26NM
## 330 0.000 2CO
## 331 0.000 2CO
## 332 1.000 18TX
## 333 0.003 19TX
## 334 0.244 28NM
## 335 0.088 28NM
## 336 0.758 26NM
## 337 0.000 2CO
## 338 0.000 2CO
## 339 0.000 2CO
## 340 0.000 2CO
## 341 0.918 27NM
## 342 0.985 27NM
## 343 0.925 27NM
## 344 0.081 19TX
## 345 1.000 27NM
## 346 0.817 26NM
## 347 0.514 26NM
## 348 0.783 26NM
## 349 0.907 26NM
## 350 1.000 21NM
## 351 0.783 21NM
## 352 0.999 21NM
## 353 0.979 21NM
## 354 0.000 2CO
## 355 0.029 19TX
## 356 0.000 2CO
## 357 0.000 2CO
## 358 0.000 2CO
## 359 0.005 19TX
## 360 0.007 19TX
## 361 0.048 19TX
## 362 0.000 19TX
## 363 0.000 4CO
## 364 0.000 4CO
## 365 0.000 4CO
## 366 0.000 2CO
## 367 0.000 4CO
## 368 1.000 18TX
## 369 0.907 18TX
## 370 0.000 2CO
## 371 0.000 2CO
## 372 0.000 2CO
## 373 0.000 2CO
## 374 0.074 19TX
## 375 0.000 19TX
## 376 0.001 19TX
## 377 0.000 2CO
## 378 0.000 19TX
## 379 0.000 4CO
## 380 0.000 4CO
## 381 0.000 4CO
## 382 0.000 4CO
## 383 0.135 19TX
## 384 0.000 19TX
## 385 0.000 19TX
## 386 0.001 19TX
## 387 0.000 4CO
## 388 0.000 2CO
## 389 0.000 4CO
## 390 0.000 4CO
## 391 1.000 18TX
## 392 0.338 18TX
## 393 0.000 18TX
## 394 0.000 18TX
## 395 0.573 28NM
## 396 0.527 28NM
## 397 0.006 28NM
## 398 0.000 2CO
## 399 0.996 26NM
## 400 0.856 26NM
## 401 1.000 26NM
## 402 0.000 28NM
## 403 0.447 28NM
## 404 0.002 46CH
## 405 0.000 46CH
## 406 0.000 46CH
## 407 0.026 46CH
## 408 0.009 46CH
## 409 0.000 46CH
## 410 0.000 46CH
## 411 0.000 46CH
## 412 0.000 46CH
## 413 0.000 46CH
## 414 0.000 46CH
## 415 0.000 46CH
## 416 0.000 46CH
## 417 0.000 46CH
## 418 0.000 46CH
## 419 0.000 46CH
## 420 0.000 46CH
## 421 0.000 46CH
## 422 0.000 46CH
## 423 0.000 46CH
## 424 0.000 46CH
## 425 0.000 46CH
## 426 0.000 46CH
## 427 0.000 46CH
## 428 0.997 51TX
## 429 1.000 51TX
## 430 1.000 51TX
## 431 1.000 51TX
## 432 0.997 51TX
## 433 1.000 51TX
## 434 1.000 51TX
## 435 1.000 51TX
## 436 1.000 51TX
## 437 1.000 51TX
## 438 1.000 51TX
## 439 1.000 51TX
## 440 1.000 51TX
## 441 1.000 51TX
## 442 1.000 50TX
## 443 1.000 50TX
## 444 1.000 50TX
## 445 1.000 50TX
## 446 0.999 50TX
## 447 1.000 50TX
## 448 1.000 50TX
## 449 1.000 50TX
## 450 1.000 49TX
## 451 1.000 49TX
## 452 1.000 49TX
## 453 1.000 49TX
## 454 0.999 49TX
## 455 1.000 49TX
## 456 1.000 49TX
## 457 1.000 49TX
## 458 1.000 49TX
## 459 1.000 49TX
## 460 1.000 49TX
## 461 0.999 49TX
## 462 1.000 49TX
## 463 1.000 49TX
## 464 1.000 49TX
## 465 1.000 49TX
## 466 1.000 49TX
## 467 1.000 49TX
## 468 1.000 49TX
## 469 1.000 49TX
## 470 1.000 49TX
## 471 1.000 49TX
## 472 0.999 49TX
## 473 1.000 49TX
## 474 0.998 49TX
## 475 1.000 49TX
## 476 1.000 49TX
## 477 1.000 47TX
## 478 0.998 47TX
## 479 0.999 47TX
## 480 1.000 47TX
## 481 1.000 47TX
## 482 1.000 47TX
## 483 1.000 47TX
## 484 1.000 47TX
## 485 1.000 47TX
## 486 0.997 47TX
## 487 0.999 47TX
## 488 1.000 47TX
## 489 1.000 47TX
## 490 1.000 47TX
## 491 1.000 47TX
## 492 0.998 47TX
## 493 0.998 47TX
## 494 1.000 47TX
## 495 0.975 47TX
## 496 1.000 47TX
## 497 1.000 47TX
## 498 1.000 47TX
## 499 0.905 47TX
## 500 1.000 47TX
## 501 1.000 47TX
## 502 0.000 CARINA_LAB
## 503 0.000 CARINA_LAB
## 504 0.000 CARINA_LAB
## 505 0.001 CARINA_LAB
## 506 0.000 CARINA_LAB
## 507 0.018 CARINA_LAB
## 508 0.000 CARINA_LAB
## 509 0.000 CARINA_LAB
## 510 0.000 CARINA_LAB
## 511 0.002 CARINA_LAB
## 512 0.006 CARINA_LAB
## 513 0.000 CARINA_LAB
## 514 0.000 CARINA_LAB
## 515 0.000 CARINA_LAB
## 516 1.000 SUB_LAB
## 517 0.999 SUB_LAB
## 518 1.000 SUB_LAB
## 519 1.000 SUB_LAB
## 520 1.000 SUB_LAB
## 521 1.000 SUB_LAB
## 522 1.000 SUB_LAB
## 523 1.000 SUB_LAB
## 524 1.000 SUB_LAB
## 525 0.996 SUB_LAB
## 526 1.000 SUB_LAB
## 527 1.000 SUB_LAB
## 528 0.998 SUB_LAB
## 529 1.000 SUB_LAB
## 530 1.000 SUB_LAB
## 531 1.000 SUB_LAB
## 532 1.000 SUB_LAB
## 533 1.000 52TX
## 534 1.000 52TX
## 535 0.998 52TX
## 536 1.000 52TX
## 537 1.000 52TX
## 538 1.000 52TX
## 539 1.000 52TX
## 540 1.000 52TX
## 541 1.000 52TX
## 542 1.000 52TX
## 543 1.000 52TX
## 544 1.000 52TX
## 545 0.999 52TX
## 546 1.000 52TX
## 547 1.000 52TX
## 548 1.000 52TX
## 549 1.000 52TX
## 550 1.000 52TX
## 551 1.000 52TX
## 552 1.000 52TX
## 553 1.000 52TXwrite.csv(ci,"ancestry_confidenceintervals.csv",
quote = FALSE)
library(tibble) # for `rownames_to_column` and `column_to_rownames`## Warning: package 'tibble' was built under R version 3.5.2colnames(ci)## [1] "sampID" "elongata_L" "elongata_H" "carinata_L"
## [5] "carinata_H" "carinulata_L" "carinulata_H" "sublineata_L"
## [9] "sublineata_H" "elongata" "carinata" "carinulata"
## [13] "sublineata" "popID"## How many tri-specific hybrids?
ci %>%
rownames_to_column('individual') %>%
filter(carinata_L >.01 & elongata_L> .01 & sublineata_L > .01) %>%
arrange(desc(elongata_L))## individual sampID elongata_L elongata_H carinata_L carinata_H
## 1 229 F84 0.022 0.055 0.050 0.128
## 2 254 G2 0.019 0.053 0.733 0.832
## 3 348 H23 0.012 0.043 0.144 0.239
## carinulata_L carinulata_H sublineata_L sublineata_H elongata carinata
## 1 0 0.001 0.837 0.911 0.037 0.087
## 2 0 0.001 0.135 0.230 0.035 0.784
## 3 0 0.001 0.736 0.828 0.026 0.190
## carinulata sublineata popID
## 1 0 0.876 26NM
## 2 0 0.181 15TX
## 3 0 0.783 26NMci %>%
rownames_to_column('individual') %>%
filter(carinata >.01 & elongata > .01 & sublineata > .01) %>%
arrange(desc(elongata))## individual sampID elongata_L elongata_H carinata_L carinata_H
## 1 229 F84 0.022 0.055 0.050 0.128
## 2 254 G2 0.019 0.053 0.733 0.832
## 3 240 F94 0.000 0.054 0.099 0.202
## 4 348 H23 0.012 0.043 0.144 0.239
## 5 223 F78 0.005 0.044 0.036 0.110
## 6 341 H17 0.000 0.045 0.000 0.112
## 7 334 H10 0.000 0.048 0.626 0.755
## carinulata_L carinulata_H sublineata_L sublineata_H elongata carinata
## 1 0.000 0.001 0.837 0.911 0.037 0.087
## 2 0.000 0.001 0.135 0.230 0.035 0.784
## 3 0.000 0.019 0.768 0.865 0.031 0.148
## 4 0.000 0.001 0.736 0.828 0.026 0.190
## 5 0.000 0.001 0.869 0.935 0.025 0.071
## 6 0.000 0.001 0.877 0.958 0.019 0.063
## 7 0.027 0.073 0.183 0.307 0.014 0.692
## carinulata sublineata popID
## 1 0.000 0.876 26NM
## 2 0.000 0.181 15TX
## 3 0.003 0.819 26NM
## 4 0.000 0.783 26NM
## 5 0.000 0.904 27NM
## 6 0.000 0.918 27NM
## 7 0.050 0.244 28NM## How many hybrids with carinulata?
ci %>%
rownames_to_column('individual') %>%
filter(carinulata_L >.01) %>%
filter(elongata_L> .01 |
sublineata_L > .01 | carinata_L > .01) %>%
arrange(desc(carinulata_L))## individual sampID elongata_L elongata_H carinata_L carinata_H
## 1 407 I04 0.000 0.001 0.000 0.002
## 2 335 H11_rep 0.000 0.024 0.000 0.001
## 3 287 G5_rep 0.000 0.001 0.311 0.378
## 4 52 D70_rep 0.860 0.909 0.000 0.001
## 5 285 G48_rep 0.000 0.001 0.000 0.001
## 6 499 N7 0.000 0.001 0.000 0.001
## 7 369 H42 0.000 0.001 0.000 0.005
## 8 4 D15_rep 0.914 0.956 0.000 0.001
## 9 14 D24_rep 0.921 0.962 0.000 0.001
## 10 310 G71 0.000 0.001 0.000 0.001
## 11 344 H2 0.000 0.001 0.817 0.914
## 12 334 H10 0.000 0.048 0.626 0.755
## 13 360 H34 0.000 0.001 0.911 0.971
## 14 333 H1 0.000 0.005 0.946 0.985
## 15 495 N3 0.000 0.001 0.000 0.001
## carinulata_L carinulata_H sublineata_L sublineata_H elongata carinata
## 1 0.962 0.983 0.016 0.038 0.000 0.000
## 2 0.888 0.926 0.066 0.109 0.004 0.000
## 3 0.621 0.683 0.000 0.023 0.000 0.345
## 4 0.090 0.139 0.000 0.002 0.885 0.000
## 5 0.071 0.112 0.888 0.929 0.000 0.000
## 6 0.071 0.120 0.880 0.929 0.000 0.000
## 7 0.067 0.118 0.879 0.932 0.000 0.001
## 8 0.039 0.078 0.000 0.028 0.936 0.000
## 9 0.038 0.079 0.000 0.001 0.942 0.000
## 10 0.033 0.066 0.934 0.967 0.000 0.000
## 11 0.033 0.076 0.032 0.130 0.000 0.866
## 12 0.027 0.073 0.183 0.307 0.014 0.692
## 13 0.027 0.066 0.000 0.042 0.000 0.948
## 14 0.013 0.047 0.000 0.019 0.001 0.967
## 15 0.012 0.039 0.961 0.987 0.000 0.000
## carinulata sublineata popID
## 1 0.973 0.026 46CH
## 2 0.908 0.088 28NM
## 3 0.652 0.003 28NM
## 4 0.114 0.000 37CR
## 5 0.091 0.909 6KS
## 6 0.094 0.905 47TX
## 7 0.091 0.907 18TX
## 8 0.058 0.006 41CR
## 9 0.058 0.000 44GR
## 10 0.049 0.951 18TX
## 11 0.054 0.081 19TX
## 12 0.050 0.244 28NM
## 13 0.045 0.007 19TX
## 14 0.029 0.003 19TX
## 15 0.025 0.975 47TXci %>%
rownames_to_column('individual') %>%
filter(carinulata_H >.1) %>%
filter(elongata_L> .01 |
sublineata_L > .01 | carinata_L > .01) %>%
arrange(desc(carinulata_L))## individual sampID elongata_L elongata_H carinata_L carinata_H
## 1 407 I04 0.00 0.001 0.000 0.002
## 2 335 H11_rep 0.00 0.024 0.000 0.001
## 3 287 G5_rep 0.00 0.001 0.311 0.378
## 4 52 D70_rep 0.86 0.909 0.000 0.001
## 5 285 G48_rep 0.00 0.001 0.000 0.001
## 6 499 N7 0.00 0.001 0.000 0.001
## 7 369 H42 0.00 0.001 0.000 0.005
## carinulata_L carinulata_H sublineata_L sublineata_H elongata carinata
## 1 0.962 0.983 0.016 0.038 0.000 0.000
## 2 0.888 0.926 0.066 0.109 0.004 0.000
## 3 0.621 0.683 0.000 0.023 0.000 0.345
## 4 0.090 0.139 0.000 0.002 0.885 0.000
## 5 0.071 0.112 0.888 0.929 0.000 0.000
## 6 0.071 0.120 0.880 0.929 0.000 0.000
## 7 0.067 0.118 0.879 0.932 0.000 0.001
## carinulata sublineata popID
## 1 0.973 0.026 46CH
## 2 0.908 0.088 28NM
## 3 0.652 0.003 28NM
## 4 0.114 0.000 37CR
## 5 0.091 0.909 6KS
## 6 0.094 0.905 47TX
## 7 0.091 0.907 18TX## How many hybrids with sublineata?
ci %>%
rownames_to_column('individual') %>%
filter(sublineata_L >.01) %>%
filter(carinulata_L > .01 |
elongata_L > .01 | carinata_L > .01) %>%
arrange(desc(sublineata_L))## individual sampID elongata_L elongata_H carinata_L carinata_H
## 1 495 N3 0.000 0.001 0.000 0.001
## 2 246 G12 0.018 0.043 0.000 0.001
## 3 256 G21 0.020 0.048 0.000 0.001
## 4 320 G81 0.000 0.001 0.011 0.056
## 5 263 G28 0.027 0.057 0.000 0.001
## 6 310 G71 0.000 0.001 0.000 0.001
## 7 257 G22 0.034 0.068 0.000 0.001
## 8 275 G39 0.028 0.070 0.000 0.023
## 9 277 G40 0.000 0.001 0.027 0.087
## 10 244 G10 0.055 0.091 0.000 0.001
## 11 288 G50 0.065 0.105 0.000 0.001
## 12 343 H19 0.000 0.001 0.047 0.106
## 13 285 G48_rep 0.000 0.001 0.000 0.001
## 14 297 G6 0.000 0.001 0.053 0.114
## 15 499 N7 0.000 0.001 0.000 0.001
## 16 369 H42 0.000 0.001 0.000 0.005
## 17 241 F95 0.000 0.001 0.054 0.126
## 18 223 F78 0.005 0.044 0.036 0.110
## 19 349 H24 0.057 0.118 0.000 0.041
## 20 271 G35 0.000 0.001 0.053 0.143
## 21 245 G11 0.000 0.001 0.073 0.156
## 22 229 F84 0.022 0.055 0.050 0.128
## 23 400 H71 0.000 0.016 0.099 0.188
## 24 301 G63 0.000 0.009 0.121 0.209
## 25 346 H21 0.000 0.001 0.140 0.227
## 26 240 F94 0.000 0.054 0.099 0.202
## 27 351 H26 0.185 0.248 0.000 0.001
## 28 329 G9 0.000 0.001 0.163 0.256
## 29 348 H23 0.012 0.043 0.144 0.239
## 30 336 H12 0.000 0.001 0.195 0.294
## 31 289 G52 0.000 0.001 0.207 0.304
## 32 322 G83 0.000 0.001 0.193 0.329
## 33 242 F96 0.000 0.015 0.269 0.384
## 34 253 G19 0.000 0.002 0.301 0.425
## 35 395 H67 0.000 0.001 0.367 0.488
## 36 396 H68 0.000 0.001 0.413 0.533
## 37 238 F92 0.000 0.001 0.419 0.541
## 38 347 H22 0.000 0.002 0.427 0.545
## 39 403 H9 0.000 0.001 0.492 0.613
## 40 274 G38 0.000 0.001 0.554 0.673
## 41 392 H64 0.000 0.001 0.604 0.721
## 42 334 H10 0.000 0.048 0.626 0.755
## 43 254 G2 0.019 0.053 0.733 0.832
## 44 383 H55 0.000 0.001 0.815 0.911
## 45 316 G78 0.000 0.001 0.827 0.918
## 46 335 H11_rep 0.000 0.024 0.000 0.001
## 47 344 H2 0.000 0.001 0.817 0.914
## 48 374 H47 0.000 0.001 0.876 0.974
## 49 407 I04 0.000 0.001 0.000 0.002
## carinulata_L carinulata_H sublineata_L sublineata_H elongata carinata
## 1 0.012 0.039 0.961 0.987 0.000 0.000
## 2 0.000 0.001 0.957 0.982 0.029 0.000
## 3 0.000 0.001 0.952 0.980 0.033 0.000
## 4 0.000 0.001 0.944 0.989 0.000 0.032
## 5 0.000 0.001 0.943 0.973 0.041 0.000
## 6 0.033 0.066 0.934 0.967 0.000 0.000
## 7 0.000 0.001 0.932 0.966 0.050 0.000
## 8 0.000 0.002 0.924 0.969 0.048 0.003
## 9 0.000 0.001 0.913 0.973 0.000 0.055
## 10 0.000 0.001 0.909 0.945 0.072 0.000
## 11 0.000 0.001 0.895 0.935 0.084 0.000
## 12 0.000 0.001 0.893 0.953 0.000 0.075
## 13 0.071 0.112 0.888 0.929 0.000 0.000
## 14 0.000 0.001 0.886 0.947 0.000 0.082
## 15 0.071 0.120 0.880 0.929 0.000 0.000
## 16 0.067 0.118 0.879 0.932 0.000 0.001
## 17 0.000 0.001 0.874 0.946 0.000 0.087
## 18 0.000 0.001 0.869 0.935 0.025 0.071
## 19 0.000 0.010 0.869 0.937 0.086 0.006
## 20 0.000 0.001 0.857 0.947 0.000 0.094
## 21 0.000 0.001 0.843 0.927 0.000 0.112
## 22 0.000 0.001 0.837 0.911 0.037 0.087
## 23 0.000 0.001 0.810 0.898 0.002 0.142
## 24 0.000 0.001 0.790 0.877 0.001 0.164
## 25 0.000 0.001 0.773 0.860 0.000 0.183
## 26 0.000 0.019 0.768 0.865 0.031 0.148
## 27 0.000 0.007 0.751 0.814 0.216 0.000
## 28 0.000 0.001 0.744 0.837 0.000 0.208
## 29 0.000 0.001 0.736 0.828 0.026 0.190
## 30 0.000 0.001 0.706 0.805 0.000 0.242
## 31 0.000 0.001 0.696 0.793 0.000 0.254
## 32 0.000 0.001 0.671 0.806 0.000 0.259
## 33 0.000 0.001 0.615 0.729 0.002 0.326
## 34 0.000 0.001 0.575 0.699 0.000 0.362
## 35 0.000 0.001 0.512 0.633 0.000 0.427
## 36 0.000 0.001 0.467 0.587 0.000 0.473
## 37 0.000 0.001 0.459 0.581 0.000 0.480
## 38 0.000 0.001 0.454 0.572 0.000 0.486
## 39 0.000 0.001 0.387 0.507 0.000 0.553
## 40 0.000 0.001 0.327 0.446 0.000 0.614
## 41 0.000 0.001 0.279 0.396 0.000 0.662
## 42 0.027 0.073 0.183 0.307 0.014 0.692
## 43 0.000 0.001 0.135 0.230 0.035 0.784
## 44 0.000 0.001 0.088 0.185 0.000 0.865
## 45 0.000 0.001 0.082 0.172 0.000 0.875
## 46 0.888 0.926 0.066 0.109 0.004 0.000
## 47 0.033 0.076 0.032 0.130 0.000 0.866
## 48 0.000 0.001 0.026 0.123 0.000 0.926
## 49 0.962 0.983 0.016 0.038 0.000 0.000
## carinulata sublineata popID
## 1 0.025 0.975 47TX
## 2 0.000 0.970 26NM
## 3 0.000 0.967 27NM
## 4 0.000 0.968 27NM
## 5 0.000 0.959 27NM
## 6 0.049 0.951 18TX
## 7 0.000 0.950 27NM
## 8 0.000 0.949 21NM
## 9 0.000 0.945 21NM
## 10 0.000 0.927 26NM
## 11 0.000 0.916 20NM
## 12 0.000 0.925 27NM
## 13 0.091 0.909 6KS
## 14 0.000 0.918 28NM
## 15 0.094 0.905 47TX
## 16 0.091 0.907 18TX
## 17 0.000 0.913 26NM
## 18 0.000 0.904 27NM
## 19 0.001 0.907 26NM
## 20 0.000 0.905 20NM
## 21 0.000 0.888 26NM
## 22 0.000 0.876 26NM
## 23 0.000 0.856 26NM
## 24 0.000 0.835 20NM
## 25 0.000 0.817 26NM
## 26 0.003 0.819 26NM
## 27 0.001 0.783 21NM
## 28 0.000 0.792 26NM
## 29 0.000 0.783 26NM
## 30 0.000 0.758 26NM
## 31 0.000 0.745 20NM
## 32 0.000 0.741 21NM
## 33 0.000 0.672 26NM
## 34 0.000 0.638 27NM
## 35 0.000 0.573 28NM
## 36 0.000 0.527 28NM
## 37 0.000 0.520 28NM
## 38 0.000 0.514 26NM
## 39 0.000 0.447 28NM
## 40 0.000 0.386 20NM
## 41 0.000 0.338 18TX
## 42 0.050 0.244 28NM
## 43 0.000 0.181 15TX
## 44 0.000 0.135 19TX
## 45 0.000 0.125 16TX
## 46 0.908 0.088 28NM
## 47 0.054 0.081 19TX
## 48 0.000 0.074 19TX
## 49 0.973 0.026 46CH## How many carinata-sublineata hybrids?
car_sub_hyb <- ci %>%
rownames_to_column('individual') %>%
filter(carinata_L >.01 & sublineata_L > .01 & elongata_L < .01)
car_sub_hyb## individual sampID elongata_L elongata_H carinata_L carinata_H
## 1 223 F78 0.005 0.044 0.036 0.110
## 2 238 F92 0.000 0.001 0.419 0.541
## 3 240 F94 0.000 0.054 0.099 0.202
## 4 241 F95 0.000 0.001 0.054 0.126
## 5 242 F96 0.000 0.015 0.269 0.384
## 6 245 G11 0.000 0.001 0.073 0.156
## 7 253 G19 0.000 0.002 0.301 0.425
## 8 271 G35 0.000 0.001 0.053 0.143
## 9 274 G38 0.000 0.001 0.554 0.673
## 10 277 G40 0.000 0.001 0.027 0.087
## 11 289 G52 0.000 0.001 0.207 0.304
## 12 297 G6 0.000 0.001 0.053 0.114
## 13 301 G63 0.000 0.009 0.121 0.209
## 14 316 G78 0.000 0.001 0.827 0.918
## 15 320 G81 0.000 0.001 0.011 0.056
## 16 322 G83 0.000 0.001 0.193 0.329
## 17 329 G9 0.000 0.001 0.163 0.256
## 18 334 H10 0.000 0.048 0.626 0.755
## 19 336 H12 0.000 0.001 0.195 0.294
## 20 343 H19 0.000 0.001 0.047 0.106
## 21 344 H2 0.000 0.001 0.817 0.914
## 22 346 H21 0.000 0.001 0.140 0.227
## 23 347 H22 0.000 0.002 0.427 0.545
## 24 374 H47 0.000 0.001 0.876 0.974
## 25 383 H55 0.000 0.001 0.815 0.911
## 26 392 H64 0.000 0.001 0.604 0.721
## 27 395 H67 0.000 0.001 0.367 0.488
## 28 396 H68 0.000 0.001 0.413 0.533
## 29 400 H71 0.000 0.016 0.099 0.188
## 30 403 H9 0.000 0.001 0.492 0.613
## carinulata_L carinulata_H sublineata_L sublineata_H elongata carinata
## 1 0.000 0.001 0.869 0.935 0.025 0.071
## 2 0.000 0.001 0.459 0.581 0.000 0.480
## 3 0.000 0.019 0.768 0.865 0.031 0.148
## 4 0.000 0.001 0.874 0.946 0.000 0.087
## 5 0.000 0.001 0.615 0.729 0.002 0.326
## 6 0.000 0.001 0.843 0.927 0.000 0.112
## 7 0.000 0.001 0.575 0.699 0.000 0.362
## 8 0.000 0.001 0.857 0.947 0.000 0.094
## 9 0.000 0.001 0.327 0.446 0.000 0.614
## 10 0.000 0.001 0.913 0.973 0.000 0.055
## 11 0.000 0.001 0.696 0.793 0.000 0.254
## 12 0.000 0.001 0.886 0.947 0.000 0.082
## 13 0.000 0.001 0.790 0.877 0.001 0.164
## 14 0.000 0.001 0.082 0.172 0.000 0.875
## 15 0.000 0.001 0.944 0.989 0.000 0.032
## 16 0.000 0.001 0.671 0.806 0.000 0.259
## 17 0.000 0.001 0.744 0.837 0.000 0.208
## 18 0.027 0.073 0.183 0.307 0.014 0.692
## 19 0.000 0.001 0.706 0.805 0.000 0.242
## 20 0.000 0.001 0.893 0.953 0.000 0.075
## 21 0.033 0.076 0.032 0.130 0.000 0.866
## 22 0.000 0.001 0.773 0.860 0.000 0.183
## 23 0.000 0.001 0.454 0.572 0.000 0.486
## 24 0.000 0.001 0.026 0.123 0.000 0.926
## 25 0.000 0.001 0.088 0.185 0.000 0.865
## 26 0.000 0.001 0.279 0.396 0.000 0.662
## 27 0.000 0.001 0.512 0.633 0.000 0.427
## 28 0.000 0.001 0.467 0.587 0.000 0.473
## 29 0.000 0.001 0.810 0.898 0.002 0.142
## 30 0.000 0.001 0.387 0.507 0.000 0.553
## carinulata sublineata popID
## 1 0.000 0.904 27NM
## 2 0.000 0.520 28NM
## 3 0.003 0.819 26NM
## 4 0.000 0.913 26NM
## 5 0.000 0.672 26NM
## 6 0.000 0.888 26NM
## 7 0.000 0.638 27NM
## 8 0.000 0.905 20NM
## 9 0.000 0.386 20NM
## 10 0.000 0.945 21NM
## 11 0.000 0.745 20NM
## 12 0.000 0.918 28NM
## 13 0.000 0.835 20NM
## 14 0.000 0.125 16TX
## 15 0.000 0.968 27NM
## 16 0.000 0.741 21NM
## 17 0.000 0.792 26NM
## 18 0.050 0.244 28NM
## 19 0.000 0.758 26NM
## 20 0.000 0.925 27NM
## 21 0.054 0.081 19TX
## 22 0.000 0.817 26NM
## 23 0.000 0.514 26NM
## 24 0.000 0.074 19TX
## 25 0.000 0.135 19TX
## 26 0.000 0.338 18TX
## 27 0.000 0.573 28NM
## 28 0.000 0.527 28NM
## 29 0.000 0.856 26NM
## 30 0.000 0.447 28NMci %>%
rownames_to_column('individual') %>%
filter(carinata_L >.01 & sublineata_L > .01 & elongata_L < .01) %>%
count()## # A tibble: 1 x 1
## n
## <int>
## 1 30mean(car_sub_hyb$sublineata)## [1] 0.6334333## How many carinata-elongata hybrids?
car_elong_hyb <- ci %>%
rownames_to_column('individual') %>%
filter(carinata_L >.01 & elongata_L> .01 & sublineata_L < .01)
ci %>%
rownames_to_column('individual') %>%
filter(carinata_L >.01 & elongata_L> .01 & sublineata_L < .01) %>%
count()## # A tibble: 1 x 1
## n
## <int>
## 1 3ci %>%
rownames_to_column('individual') %>%
filter(carinata_L >.01 & elongata_L> .01 & sublineata_L < .01) %>%
summarize_at(vars(carinata_L, elongata_L), funs(mean))## carinata_L elongata_L
## 1 0.7993333 0.1346667## How many elong-sublineata hybrids?
elong_sub_hyb <- ci %>%
rownames_to_column('individual') %>%
filter(carinata_L < .01 & sublineata_L > .01 & elongata_L > .01)
elong_sub_hyb## individual sampID elongata_L elongata_H carinata_L carinata_H
## 1 244 G10 0.055 0.091 0 0.001
## 2 246 G12 0.018 0.043 0 0.001
## 3 256 G21 0.020 0.048 0 0.001
## 4 257 G22 0.034 0.068 0 0.001
## 5 263 G28 0.027 0.057 0 0.001
## 6 275 G39 0.028 0.070 0 0.023
## 7 288 G50 0.065 0.105 0 0.001
## 8 349 H24 0.057 0.118 0 0.041
## 9 351 H26 0.185 0.248 0 0.001
## carinulata_L carinulata_H sublineata_L sublineata_H elongata carinata
## 1 0 0.001 0.909 0.945 0.072 0.000
## 2 0 0.001 0.957 0.982 0.029 0.000
## 3 0 0.001 0.952 0.980 0.033 0.000
## 4 0 0.001 0.932 0.966 0.050 0.000
## 5 0 0.001 0.943 0.973 0.041 0.000
## 6 0 0.002 0.924 0.969 0.048 0.003
## 7 0 0.001 0.895 0.935 0.084 0.000
## 8 0 0.010 0.869 0.937 0.086 0.006
## 9 0 0.007 0.751 0.814 0.216 0.000
## carinulata sublineata popID
## 1 0.000 0.927 26NM
## 2 0.000 0.970 26NM
## 3 0.000 0.967 27NM
## 4 0.000 0.950 27NM
## 5 0.000 0.959 27NM
## 6 0.000 0.949 21NM
## 7 0.000 0.916 20NM
## 8 0.001 0.907 26NM
## 9 0.001 0.783 21NMmean(elong_sub_hyb$sublineata)## [1] 0.9253333### this is probably better represented as a simplex (triangle)
pCS <- ggplot(car_sub_hyb) +
geom_histogram(aes(carinata),
alpha = .5, fill = legend[which(legend$spp=="carinata"), "cbbPalette"], stat = "bin", binwidth = .05) +
geom_histogram(aes(sublineata),
alpha = .5, fill = legend[which(legend$spp=="sublineata"), "cbbPalette"], stat = "bin", binwidth = .05) +
ylim(c(0,8)) +
scale_x_continuous(name= expression( ~italic("D. carinata")~ "X" ~italic("D. sublineata")~ "q-values")) +
theme_bw()
pCE <-ggplot(car_elong_hyb) +
geom_histogram(aes(carinata),
alpha = .5, fill = legend[which(legend$spp=="carinata"), "cbbPalette"], stat = "bin", binwidth = .05) +
geom_histogram(aes(elongata),
alpha = .5, fill = legend[which(legend$spp=="elongata"), "cbbPalette"], stat = "bin", binwidth = .05) +
ylim(c(0,8)) +
scale_x_continuous(name= expression( ~italic("D. elongata")~ "X" ~italic(" D. carinata")~ "q-values")) +
theme_bw()
pCE
pES <-ggplot(elong_sub_hyb) +
geom_histogram(aes(elongata),
alpha = .5,fill = legend[which(legend$spp=="elongata"), "cbbPalette"], stat = "bin", binwidth = .05) +
geom_histogram(aes(sublineata),
alpha = .5, fill = legend[which(legend$spp=="sublineata"), "cbbPalette"], stat = "bin", binwidth = .05) +
ylim(c(0,8)) +
scale_x_continuous(name= expression( ~italic("D. elongata")~ "X" ~italic(" D. sublineata")~ "q-values")) +
theme_bw()
cowplot::plot_grid(pCS, pCE, pES, nrow = 1, labels = c('A','B','C'))
ggsave("hybrid_distributions.jpg", dpi = 300, height = 4, width = 10, units = "in")## Pull pure parental species
pure_parentals <- ci %>%
filter(carinata_L > .995 | elongata_L > .995 |
sublineata_L > .995 | carinulata_L > .995) %>%
merge(popmap)
pure_parentals$assignment <- colnames(pure_parentals[,c('elongata', 'carinata', 'carinulata', 'sublineata')])[max.col(pure_parentals[,c('elongata', 'carinata', 'carinulata', 'sublineata')])]
table(pure_parentals$assignment)##
## carinata carinulata elongata sublineata
## 40 172 86 129pure_parentals_popmap <- pure_parentals[,c('sampID', 'assignment')]
write.table(pure_parentals_popmap, "../info/pure_parentals_popmap.tsv", col.names = F, quote = F, row.names = F, sep = "\t")Substructure
Population structure within D. carinulata
sfiles <- list.files(path="~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/carinulata/structure_analysis/Results/",
pattern=glob2rx("outfile_*f"),full.names=TRUE)
carinu_slist <- readQ(sfiles,filetype="structure",
indlabfromfile = TRUE,
readci = TRUE)
sr1 <- summariseQ(tabulateQ(carinu_slist))
p <- evannoMethodStructure(data=sr1,exportplot=F,returnplot=T,returndata=F,basesize=12,linesize=0.7)
grid.arrange(p)
evannoMethodStructure(data=sr1,
exportplot=T,
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/carinulata/structure_analysis/plots/",
outputfilename = "carinulata_deltaK",
returndata=F,
height = 10, width = 9)
popmap <- left_join(data.frame(sampID = rownames(carinu_slist[[1]])),
masterpopmap)## Joining, by = "sampID"## Warning: Column `sampID` joining factor and character vector, coercing into
## character vectorpopID <- data.frame(popID = popmap$popID)
popID <- data.frame(lapply(popID, as.character), stringsAsFactors=FALSE)
sapply(popID, is.character)## popID
## TRUEpop_order <- sample_meta.dat[,c("popID", "Order")]
pop_order <- semi_join(pop_order, popID) %>%
arrange(Order)## Joining, by = "popID"pop_order <- pop_order[,1]
legend_colors## cbbPalette human_colors spp
## 1 #56B4E9 blue carinata
## 2 #E69F00 orange elongata
## 3 #009E73 green sublineata
## 4 #F0E442 yellow carinulata
## 5 #0072B2 dark blue elongata_sub
## 6 #D55E00 red carinulata_sub
## 7 #CC79A7 pink othercarinu_legend <- legend_colors[c(4,6,7),]
carinu_cbbPalette <- carinu_legend[,'cbbPalette']
plotQ(alignK(carinu_slist[c(21:30)]),
imgoutput="join",
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/carinulata/structure_analysis/plots/",
outputfilename = "Joined-K2",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=carinu_cbbPalette,
subsetgrp = pop_order,
height = .1,
ordergrp = T,
grplab = popID,
linepos = 1,
divtype = 1,
grplabangle=45,
grplabpos = .8,
grplabspacer = 0,
grplabheight=70,
width=100,
showtitle=T,
grplabsize = 4,
titlelab="D. carinulata Population Structure, K=2",
titlesize = 20)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/carinulata/structure_analysis/plots/Joined-K2.png exported.plotQ(alignK(carinu_slist[c(31:40)]),
imgoutput="join",
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/carinulata/structure_analysis/plots/",
outputfilename = "Joined-K3",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=carinu_cbbPalette,
subsetgrp = pop_order,
height = .1,
ordergrp = T,
grplab = popID,
linepos = 1,
divtype = 1,
grplabangle=45,
grplabpos = .8,
grplabspacer = 0,
grplabheight=70,
width=100,
showtitle=T,
grplabsize = 4,
titlelab="D. carinulata Population Structure, K=3",
titlesize = 20)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/carinulata/structure_analysis/plots/Joined-K3.png exported.k4 <- plotQ(alignK(carinu_slist[c(41:50)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
subsetgrp = pop_order,
ordergrp = T,
grplab = popID,
grplabangle=-90)
grid.arrange(k4$plot[[1]])
k5 <- plotQ(alignK(carinu_slist[c(51:60)]),
imgoutput="join",
subsetgrp = pop_order,
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
ordergrp = T,
grplab = popID,
grplabangle=-90)
grid.arrange(k5$plot[[1]])
k6 <- plotQ(alignK(carinu_slist[c(61:70)]),
imgoutput="join",
subsetgrp = pop_order,
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
ordergrp = T,
grplab = popID,
grplabangle=-90)
grid.arrange(k6$plot[[1]])
k7 <- plotQ(alignK(carinu_slist[c(71:80)]),
imgoutput="join",
subsetgrp = pop_order,
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
ordergrp = T,
grplab = popID,
grplabangle=-90)
grid.arrange(k7$plot[[1]])
plotQ(carinu_slist[31],
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/carinulata/structure_analysis/plots/",
outputfilename = "MainTextFigure_carinuK3",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=carinu_cbbPalette,
subsetgrp = pop_order,
ordergrp = T,
grplab = popID,
linepos = 1,
linesize=0.8,
pointsize = 5,
divtype = 1,
divsize = 1,
grplabangle= 90,
grplabpos = .9,
grplabspacer = 0,
grplabheight=40,
grplabsize = 25,
height = .05,
width=100,
showlegend = T, legendkeysize=30,legendtextsize=30, legendpos="left", legendlab= c("D. carinulata Fukang Ecotype", "D. carinulata Chilik Ecotype", "Other"),
basesize=30)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/carinulata/structure_analysis/plots/MainTextFigure_carinuK3.png exported.Population structure within D. elongata
sfiles <- list.files(path="~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/elongata/structure_analysis/Results/",
pattern="outfile_*",full.names=TRUE)
elong_slist <- readQ(sfiles,filetype="structure",
indlabfromfile = TRUE,
readci = TRUE)
popmap <- left_join(data.frame(sampID = rownames(elong_slist[[1]])),
masterpopmap)## Joining, by = "sampID"## Warning: Column `sampID` joining factor and character vector, coercing into
## character vectorpopID <- data.frame(popID = popmap$popID)
popID <- data.frame(lapply(popID, as.character), stringsAsFactors=FALSE)
sapply(popID, is.character)## popID
## TRUEpop_order <- sample_meta.dat[,c("popID", "Order")]
pop_order <- semi_join(pop_order, popID) %>%
arrange(Order)## Joining, by = "popID"pop_order <- pop_order[,1]
legend_colors## cbbPalette human_colors spp
## 1 #56B4E9 blue carinata
## 2 #E69F00 orange elongata
## 3 #009E73 green sublineata
## 4 #F0E442 yellow carinulata
## 5 #0072B2 dark blue elongata_sub
## 6 #D55E00 red carinulata_sub
## 7 #CC79A7 pink otherelong_legend <- legend_colors[c(2,5,7),]
elong_cbbPalette <- elong_legend[,'cbbPalette']sr1 <- summariseQ(tabulateQ(elong_slist))
evannoMethodStructure(data=sr1,
exportplot=T,
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/elongata/structure_analysis/plots/",
outputfilename = "elongata_deltaK",
returndata=F,
height = 10, width = 9)
k2 <- plotQ(alignK(elong_slist[c(21:30)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
subsetgrp = pop_order,
ordergrp = T,
grplab = popID,
linepos = 1,
grplabangle=-45,
grplabpos = 0,
grplabheight=20)
grid.arrange(k2$plot[[1]])
k3 <- plotQ(alignK(elong_slist[c(31:40)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
ordergrp = T,
grplab = popID,
grplabangle=-90)
grid.arrange(k3$plot[[1]])
k4 <- plotQ(alignK(elong_slist[c(41:50)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
ordergrp = T,
grplab = popID,
grplabangle=-90)
grid.arrange(k4$plot[[1]])
k5 <- plotQ(alignK(elong_slist[c(51:60)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
ordergrp = T,
grplab = popID,
grplabangle=-90)
grid.arrange(k5$plot[[1]])
k6 <- plotQ(alignK(elong_slist[c(61:70)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
ordergrp = T,
grplab = popID,
grplabangle=-90)
grid.arrange(k6$plot[[1]])
k7 <- plotQ(alignK(elong_slist[c(71:80)]),
imgoutput="join",
returnplot=T,exportplot=F,quiet=T,basesize=11,
clustercol=cbbPalette,
ordergrp = T,
grplab = popID,
grplabangle=-90)
grid.arrange(k7$plot[[1]])
plotQ(elong_slist[32],
exportpath = "~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/elongata/structure_analysis/plots/",
outputfilename = "MainTextFigure_elongataK3",
exportplot=T,
showyaxis=T,
showsp = F,
clustercol=elong_cbbPalette,
subsetgrp = pop_order,
ordergrp = T,
grplab = popID,
linepos = 1,
linesize=0.8,
pointsize = 5,
divtype = 1,
divsize = 1,
grplabangle= 90,
grplabpos = .9,
grplabspacer = 0,
grplabheight=40,
grplabsize = 25,
height = .05,
width=100,
showlegend = T, legendkeysize=30,legendtextsize=30, legendpos="left", legendlab= c("D. elongata Mainland Ecotype", "D. elongata Crete Ecotype", "Other"),
basesize=30)## Drawing plot ...## ~/Code/diorhabda/StahlkeBitume_heirarchical_str/Git_Repo/substructure/elongata/structure_analysis/plots/MainTextFigure_elongataK3.png exported.